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A

AB_FILTER - Static variable in class picard.vcf.filter.AlleleBalanceFilter
The filter string used for sites that fail the allele balance filter.
AbstractAlignmentMerger - Class in picard.sam
Abstract class that coordinates the general task of taking in a set of alignment information, possibly in SAM format, possibly in other formats, and merging that with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
AbstractAlignmentMerger(File, File, File, boolean, boolean, boolean, SAMProgramRecord, List<String>, List<String>, Integer, Integer, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean) - Constructor for class picard.sam.AbstractAlignmentMerger
Constructor
AbstractIlluminaPositionFileReader - Class in picard.illumina.parser.readers
The position files of Illumina are nearly the same form: Pos files consist of text based tabbed x-y coordinate float pairs, locs files are binary x-y float pairs, clocs are compressed binary x-y float pairs.
AbstractIlluminaPositionFileReader(File) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
 
AbstractIlluminaPositionFileReader(File, int, int) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
Use this ctor if lane and tile are not discernible from file name.
AbstractIlluminaPositionFileReader.PositionInfo - Class in picard.illumina.parser.readers
 
AbstractIlluminaPositionFileReader.PositionInfo(float, float, int, int) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
 
AbstractInputParser - Class in picard.util
Class for parsing text files where each line consists of fields separated by whitespace.
AbstractInputParser() - Constructor for class picard.util.AbstractInputParser
 
AbstractMarkDuplicatesCommandLineProgram - Class in picard.sam.markduplicates.util
Abstract class that holds parameters and methods common to classes that perform duplicate detection and/or marking within SAM/BAM files.
AbstractMarkDuplicatesCommandLineProgram() - Constructor for class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator - Class in picard.sam.markduplicates.util
Little class used to package up a header and an iterable/iterator.
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator(SAMFileHeader, CloseableIterator<SAMRecord>) - Constructor for class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
 
AbstractOpticalDuplicateFinderCommandLineProgram - Class in picard.sam.markduplicates.util
Abstract class that holds parameters and methods common to classes that optical duplicate detection.
AbstractOpticalDuplicateFinderCommandLineProgram() - Constructor for class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectAlignmentSummaryMetrics
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectBaseDistributionByCycle
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectGcBiasMetrics
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectInsertSizeMetrics
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectRnaSeqMetrics
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.MeanQualityByCycle
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.QualityScoreDistribution
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.SinglePassSamProgram
Should be implemented by subclasses to accept SAMRecords one at a time.
acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.AlignmentSummaryMetricsCollector
 
acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.GcBiasMetricsCollector
 
acceptRecord(GcBiasCollectorArgs) - Method in class picard.analysis.directed.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
 
acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
 
acceptRecord(InsertSizeCollectorArgs) - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
 
acceptRecord(SAMRecord) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
Adds information about an individual SAMRecord to the statistics.
acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.metrics.MultiLevelCollector
Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record
acceptRecord(ARGTYPE) - Method in interface picard.metrics.PerUnitMetricCollector
Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
accumulate(VariantContext) - Method in class picard.vcf.CallingMetricAccumulator
Incorporates the provided variant's data into the metric analysis.
accumulate(VariantContext) - Method in interface picard.vcf.processor.VariantProcessor.Accumulator
 
ACCUMULATION_LEVEL - Variable in class picard.analysis.GcBiasDetailMetrics
 
ACCUMULATION_LEVEL - Variable in class picard.analysis.GcBiasSummaryMetrics
 
accumulators() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
Returns the VariantProcessor.Accumulators associated with this executor.
accumulators() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
 
ACTION - Variable in class picard.util.IntervalListTools
 
ADAPTER_SEQUENCE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
 
ADAPTER_TRUNCATION_LENGTH - Variable in class picard.illumina.MarkIlluminaAdapters
 
AdapterMarker - Class in picard.util
Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords.
AdapterMarker(AdapterPair...) - Constructor for class picard.util.AdapterMarker
Truncates adapters to DEFAULT_ADAPTER_LENGTH
AdapterMarker(int, AdapterPair...) - Constructor for class picard.util.AdapterMarker
 
AdapterPair - Interface in picard.util
 
ADAPTERS - Variable in class picard.illumina.MarkIlluminaAdapters
 
ADAPTERS_TO_CHECK - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
ADAPTERS_TO_CHECK - Variable in class picard.illumina.IlluminaBasecallsToSam
 
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord) - Method in class picard.util.AdapterMarker
 
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double) - Method in class picard.util.AdapterMarker
Overrides defaults for minMatchBases and maxErrorRate
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair) - Static method in class picard.util.ClippingUtility
Deprecated.
Use the varargs version. This no longer returns a warning string..
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair, int, double) - Static method in class picard.util.ClippingUtility
Deprecated.
Use the varargs version. This no longer returns a warning string..
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair...) - Static method in class picard.util.ClippingUtility
Invokes adapterTrimIlluminaPairedReads with default less stringent parameters for a pair of reads.
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double, AdapterPair...) - Static method in class picard.util.ClippingUtility
Invokes adapterTrimIlluminaRead with explicit parameters for a pair of reads.
adapterTrimIlluminaSingleRead(SAMRecord) - Method in class picard.util.AdapterMarker
 
adapterTrimIlluminaSingleRead(SAMRecord, int, double) - Method in class picard.util.AdapterMarker
Overrides defaults for minMatchBases and maxErrorRate
adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair) - Static method in class picard.util.ClippingUtility
Deprecated.
Use the varargs version. This no longer returns a warning string..
adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair, int, double) - Static method in class picard.util.ClippingUtility
Deprecated.
Use the varargs version. This no longer returns a warning string..
adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair...) - Static method in class picard.util.ClippingUtility
Invokes adapterTrimIlluminRead with default parameters for a single read.
adapterTrimIlluminaSingleRead(SAMRecord, int, double, AdapterPair...) - Static method in class picard.util.ClippingUtility
Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read.
add(PedFile.PedTrio) - Method in class picard.pedigree.PedFile
Adds a trio to the PedFile keyed by the individual id.
add(ReadEndsForMateCigar, SamRecordTrackingBuffer, DuplicationMetrics) - Method in class picard.sam.markduplicates.util.MarkQueue
Add a record to the mark queue.
add(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
Adds the end to this set, if not already added based on physical location
ADD_MATE_CIGAR - Variable in class picard.sam.FixMateInformation
 
ADD_MATE_CIGAR - Variable in class picard.sam.MergeBamAlignment
 
addAllLevelsToFile(MetricsFile<METRIC_TYPE, Histogram_KEY>) - Method in class picard.metrics.MultiLevelCollector
Add all metrics to the given file in the following MetricAccumulationLevel order ALL_READS, SAMPLE, LIBRARY, READ_GROUP.
addBase(int) - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
Adds a single point of depth at the desired offset into the coverage array.
AddCommentsToBam - Class in picard.sam
A tool to add comments to a BAM file header.
AddCommentsToBam() - Constructor for class picard.sam.AddCommentsToBam
 
addCoverageCounts(int, int, int[]) - Method in class picard.annotation.Gene.Transcript
 
addExon(int, int) - Method in class picard.annotation.Gene.Transcript
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.BciFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.BclFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.ClocsFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.FileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.FilterFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.LocsFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.PosFileFaker
 
addLocationInformation(String, OpticalDuplicateFinder.PhysicalLocation) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
Method used to extract tile/x/y from the read name and add it to the PhysicalLocation so that it can be used later to determine optical duplication
addLocationInformation(String, PhysicalLocation) - Method in class picard.sam.util.PhysicalLocation
Method used to extract tile/x/y from the read name and add it to the PhysicalLocation so that it can be used later to determine optical duplication
addMetricsByLibrary(String, DuplicationMetrics) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
addMetricsToFile(MetricsFile<GcBiasMetrics, Integer>) - Method in class picard.analysis.directed.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
 
addMetricsToFile(MetricsFile<InsertSizeMetrics, Integer>) - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
 
addMetricsToFile(MetricsFile<METRIC_TYPE, Integer>) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
 
addMetricsToFile(MetricsFile<BEAN, HKEY>) - Method in interface picard.metrics.PerUnitMetricCollector
Any metrics collected will be added to the metric file provided.
AddOrReplaceReadGroups - Class in picard.sam
Replaces read groups in a BAM file
AddOrReplaceReadGroups() - Constructor for class picard.sam.AddOrReplaceReadGroups
 
addRow(GenotypeConcordanceStates.CallState, GenotypeConcordanceStates.ContingencyState[]...) - Method in class picard.vcf.GenotypeConcordanceScheme
Adds a row to the scheme
addTranscript(String, int, int, int, int, int) - Method in class picard.annotation.Gene
 
advance() - Method in class picard.util.AbstractInputParser
 
advanceFile() - Method in class picard.util.BasicInputParser
 
ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
 
ALIGNED_READS - Variable in class picard.analysis.GcBiasSummaryMetrics
The total number of aligned reads used to compute the gc bias metrics.
ALIGNED_READS_ONLY - Variable in class picard.analysis.CollectBaseDistributionByCycle
 
ALIGNED_READS_ONLY - Variable in class picard.analysis.MeanQualityByCycle
 
ALIGNED_READS_ONLY - Variable in class picard.analysis.QualityScoreDistribution
 
ALIGNED_READS_ONLY - Variable in class picard.sam.MergeBamAlignment
 
ALIGNER_PROPER_PAIR_FLAGS - Variable in class picard.sam.MergeBamAlignment
 
ALIGNMENT_STATUS - Variable in class picard.sam.ViewSam
 
AlignmentSummaryMetrics - Class in picard.analysis
High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file with the extension ".alignment_summary_metrics".
AlignmentSummaryMetrics() - Constructor for class picard.analysis.AlignmentSummaryMetrics
 
AlignmentSummaryMetrics.Category - Enum in picard.analysis
 
AlignmentSummaryMetricsCollector - Class in picard.analysis
 
AlignmentSummaryMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, boolean, List<String>, int, boolean) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector
 
ALL_GTS_FILTERED - Static variable in class picard.vcf.filter.FilterApplyingVariantIterator
Filter string that is used to filter a Variant when all variant genotypes are filtered out.
AlleleBalanceFilter - Class in picard.vcf.filter
Filters out a record if the allele balance for heterozygotes is out of a defined range across all samples.
AlleleBalanceFilter(double) - Constructor for class picard.vcf.filter.AlleleBalanceFilter
 
ALLOW_AND_IGNORE_EMPTY_LINES - Variable in class picard.sam.FastqToSam
 
ALLOW_CONTIG_LENGTH_DISCORDANCE - Variable in class picard.sam.ReorderSam
 
ALLOW_INCOMPLETE_DICT_CONCORDANCE - Variable in class picard.sam.ReorderSam
 
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS - Variable in class picard.sam.PositionBasedDownsampleSam
 
ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The (upper-case) alternative base that is called as a result of DNA damage.
ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The (upper-case) alternative base that is called as a result of DNA damage.
ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The (upper-case) alternative base that is called as a result of DNA damage.
ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The (upper-case) alternative base that is called as a result of DNA damage.
ALT_NONOXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that rules out oxidation as the cause
ALT_OXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that is consistent with oxidative damage.
AMPLICON_INTERVALS - Variable in class picard.analysis.directed.CollectTargetedPcrMetrics
 
AMPLICON_TERRITORY - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of unique bases covered by the intervals of all amplicons in the amplicon set
ANALYSIS_DIR - Variable in class picard.fastq.BamToBfq
 
AnnotationException - Exception in picard.annotation
Exception thrown when loading gene annotations.
AnnotationException(String) - Constructor for exception picard.annotation.AnnotationException
 
AnnotationException(String, Throwable) - Constructor for exception picard.annotation.AnnotationException
 
APPLY_EAMSS_FILTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
APPLY_EAMSS_FILTER - Variable in class picard.illumina.IlluminaBasecallsToSam
 
areEqual() - Method in class picard.sam.CompareSAMs
 
ARTIFACT_NAME - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
A "nickname" of this artifact, if it is a known error mode.
ARTIFACT_NAME - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
A "nickname" of this artifact, if it is a known error mode.
assertEqualDoubleArrays(double[], double[], double) - Static method in class picard.util.TestNGUtil
 
assertMinimumQualities() - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
Reviews the qualities observed thus far and throws an exception if any are below the minimum quality threshold.
assertProperFileStructure(File) - Method in class picard.illumina.parser.readers.BclReader
 
assertSorted(SAMFileHeader.SortOrder) - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
Establishes that records returned by this iterator are expected to be in the specified sort order.
assignLocusFunctionForRange(int, LocusFunction[]) - Method in class picard.annotation.Gene.Transcript
Write into locusFunctions the function of each position from start to start + locusFunctions.length relative to this transcript.
ASSUME_SORTED - Variable in class picard.analysis.CollectMultipleMetrics
 
ASSUME_SORTED - Variable in class picard.analysis.CollectRrbsMetrics
 
ASSUME_SORTED - Variable in class picard.analysis.SinglePassSamProgram
 
ASSUME_SORTED - Variable in class picard.sam.FixMateInformation
 
ASSUME_SORTED - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
ASSUME_SORTED - Variable in class picard.sam.MergeSamFiles
 
ASSUME_SORTED_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
AsyncIterator<T> - Class in picard.util
Wrapper around a CloseableIterator that reads in a separate thread, for cases in which that might be efficient.
AsyncIterator(CloseableIterator<T>, int, String) - Constructor for class picard.util.AsyncIterator
 
AT_DROPOUT - Variable in class picard.analysis.directed.HsMetrics
A measure of how undercovered <= 50% GC regions are relative to the mean.
AT_DROPOUT - Variable in class picard.analysis.directed.TargetedPcrMetrics
A measure of how undercovered <= 50% GC regions are relative to the mean.
AT_DROPOUT - Variable in class picard.analysis.GcBiasSummaryMetrics
Illumina-style AT dropout metric.
AtomicIterator<T> - Interface in picard.util
Describes
atomicIteratorOf(Iterable<E>) - Static method in class picard.util.Iterators
 
atomicIteratorOf(Iterator<E>) - Static method in class picard.util.Iterators
 
ATTRIBUTE_TO_CLEAR - Variable in class picard.sam.RevertSam
 
ATTRIBUTES_TO_REMOVE - Variable in class picard.sam.MergeBamAlignment
 
ATTRIBUTES_TO_RETAIN - Variable in class picard.sam.MergeBamAlignment
 
awaitCompletion() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
Blocks until the work is complete.
awaitCompletion() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
 

B

BAD_CYCLES - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of instrument cycles in which 80% or more of base calls were no-calls.
BAIT_BIAS_DETAILS_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
 
BAIT_BIAS_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
 
BAIT_DESIGN_EFFICIENCY - Variable in class picard.analysis.directed.HsMetrics
Target terrirtoy / bait territory.
BAIT_INTERVALS - Variable in class picard.analysis.directed.CalculateHsMetrics
 
BAIT_OFFSET - Variable in class picard.util.BaitDesigner
 
BAIT_SET - Variable in class picard.analysis.directed.HsMetrics
The name of the bait set used in the hybrid selection.
BAIT_SET_NAME - Variable in class picard.analysis.directed.CalculateHsMetrics
 
BAIT_SIZE - Variable in class picard.util.BaitDesigner
 
BAIT_TERRITORY - Variable in class picard.analysis.directed.HsMetrics
The number of bases which have one or more baits on top of them.
BaitDesigner - Class in picard.util
Designs baits for hybrid selection!
BaitDesigner() - Constructor for class picard.util.BaitDesigner
 
BaitDesigner.DesignStrategy - Enum in picard.util
Set of possible design strategies for bait design.
BamIndexStats - Class in picard.sam
Command line program to print statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate.
BamIndexStats() - Constructor for class picard.sam.BamIndexStats
 
BamToBfq - Class in picard.fastq
CommandLineProgram to generate to bfq files for use by the Maq aligner
BamToBfq() - Constructor for class picard.fastq.BamToBfq
 
BamToBfqWriter - Class in picard.fastq
Class to take unmapped reads in BAM file format and create Maq binary fastq format file(s) -- one or two of them, depending on whether it's a paired-end read.
BamToBfqWriter(File, String, Integer, Integer, boolean, String, boolean, boolean, Integer) - Constructor for class picard.fastq.BamToBfqWriter
Constructor
BamToBfqWriter(File, String, boolean, String, boolean) - Constructor for class picard.fastq.BamToBfqWriter
Constructor
BARCODE - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
BARCODE - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
The barcode (from the set of expected barcodes) for which the following metrics apply.
Barcode - Static variable in enum picard.illumina.parser.ReadType
 
BARCODE_DELIMITER - Static variable in class picard.util.IlluminaUtil
 
BARCODE_FILE - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
BARCODE_NAME - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
 
BARCODE_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToSam
 
barcodeBytes - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
 
BarcodeFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
BarcodeFileFaker() - Constructor for class picard.illumina.parser.fakers.BarcodeFileFaker
 
BarcodeFileReader - Class in picard.illumina.parser.readers
Reads a single barcode file line by line and returns the barcode if there was a match or NULL otherwise.
BarcodeFileReader(File) - Constructor for class picard.illumina.parser.readers.BarcodeFileReader
 
barcodes - Variable in class picard.illumina.parser.ReadStructure
 
BARCODES_DIR - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
BARCODES_DIR - Variable in class picard.illumina.IlluminaBasecallsToSam
 
barcodeSeqsToString(List<String>) - Static method in class picard.util.IlluminaUtil
Concatenates all the barcode sequences with BARCODE_DELIMITER
barcodeSeqsToString(String[]) - Static method in class picard.util.IlluminaUtil
Concatenates all the barcode sequences with BARCODE_DELIMITER
barcodeSeqsToString(byte[][]) - Static method in class picard.util.IlluminaUtil
Concatenates all the barcode sequences with BARCODE_DELIMITER
base - Variable in class picard.illumina.parser.ParameterizedFileUtil
If you think of the file system as a tree, this is the deepest directory(node) on the tree that still contains all of the files for this given type (e.g.
BASECALLS_DIR - Variable in class picard.illumina.CheckIlluminaDirectory
 
BASECALLS_DIR - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
 
BASECALLS_DIR - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
BASECALLS_DIR - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
BASECALLS_DIR - Variable in class picard.illumina.IlluminaBasecallsToSam
 
BASECALLS_DIR - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
BaseDistributionByCycleMetrics - Class in picard.analysis
 
BaseDistributionByCycleMetrics() - Constructor for class picard.analysis.BaseDistributionByCycleMetrics
 
bases - Variable in class picard.illumina.parser.BclData
 
BASES_TO_WRITE - Variable in class picard.fastq.BamToBfq
 
BasicInputParser - Class in picard.util
TextFileParser which reads a single text file.
BasicInputParser(boolean, InputStream...) - Constructor for class picard.util.BasicInputParser
Constructor.
BasicInputParser(boolean, int, InputStream...) - Constructor for class picard.util.BasicInputParser
 
BasicInputParser(boolean, File...) - Constructor for class picard.util.BasicInputParser
Constructor.
BasicInputParser(boolean, int, File...) - Constructor for class picard.util.BasicInputParser
Constructor.
bci - Variable in class picard.illumina.parser.MultiTileFileUtil
 
BciFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/14/14.
BciFileFaker() - Constructor for class picard.illumina.parser.fakers.BciFileFaker
 
BclData - Class in picard.illumina.parser
A class that implements the IlluminaData interfaces provided by this parser One BclData object is returned to IlluminaDataProvider per cluster and each first level array in bases and qualities represents a single read in that cluster
BclData(int[]) - Constructor for class picard.illumina.parser.BclData
 
BclFileFaker - Class in picard.illumina.parser.fakers
 
BclFileFaker() - Constructor for class picard.illumina.parser.fakers.BclFileFaker
 
BclIndexReader - Class in picard.illumina.parser.readers
Annoyingly, there are two different files with extension .bci in NextSeq output.
BclIndexReader(File) - Constructor for class picard.illumina.parser.readers.BclIndexReader
 
BclQualityEvaluationStrategy - Class in picard.illumina.parser.readers
Describes a mechanism for revising and evaluating qualities read from a BCL file.
BclQualityEvaluationStrategy(int) - Constructor for class picard.illumina.parser.readers.BclQualityEvaluationStrategy
 
BclReader - Class in picard.illumina.parser.readers
BCL Files are base call and quality score binary files containing a (base,quality) pair for successive clusters.
BclReader(List<File>, int[], BclQualityEvaluationStrategy, boolean) - Constructor for class picard.illumina.parser.readers.BclReader
 
BclReader(File, BclQualityEvaluationStrategy, boolean) - Constructor for class picard.illumina.parser.readers.BclReader
 
BedToIntervalList - Class in picard.util
 
BedToIntervalList() - Constructor for class picard.util.BedToIntervalList
 
BestEndMapqPrimaryAlignmentStrategy - Class in picard.sam
For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and make that the primary.
BestEndMapqPrimaryAlignmentStrategy() - Constructor for class picard.sam.BestEndMapqPrimaryAlignmentStrategy
 
BestMapqPrimaryAlignmentSelectionStrategy - Class in picard.sam
This strategy was designed for TopHat output, but could be of general utility.
BestMapqPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.BestMapqPrimaryAlignmentSelectionStrategy
 
BLOCK_SIZE - Variable in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
 
BREAK_BANDS_AT_MULTIPLES_OF - Variable in class picard.util.IntervalListTools
 
BUFFER_SIZE - Variable in class picard.util.FifoBuffer
 
bufferSize() - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.BciFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.BclFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.ClocsFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.FileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.FilterFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.LocsFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.PosFileFaker
 
build() - Method in interface picard.vcf.processor.VariantProcessor.AccumulatorGenerator
 
build() - Method in class picard.vcf.processor.VariantProcessor.Builder
 
BuildBamIndex - Class in picard.sam
Command line program to generate a BAM index (.bai) file from a BAM (.bam) file
BuildBamIndex() - Constructor for class picard.sam.BuildBamIndex
 
byHundredMegabaseChunks(List<File>) - Static method in class picard.vcf.processor.VariantIteratorProducer
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).
byHundredMegabaseChunksWithOnTheFlyFilteringByInterval(List<File>, IntervalList) - Static method in class picard.vcf.processor.VariantIteratorProducer
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached), that also performs on-the-fly filtering of VariantContext
ByIntervalListVariantContextIterator - Class in picard.vcf
Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals.
ByIntervalListVariantContextIterator(VCFFileReader, IntervalList) - Constructor for class picard.vcf.ByIntervalListVariantContextIterator
 
byWholeContigSubdividingWithWidth(long) - Static method in class picard.vcf.processor.VcfFileSegmentGenerator
 

C

C_QUALITY_THRESHOLD - Variable in class picard.analysis.CollectRrbsMetrics
 
C_REF_ALT_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The number of alt (A/T) basecalls observed at sites where the genome reference == C.
C_REF_OXO_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there were no bias between sites with a C reference base vs.
C_REF_OXO_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
C_REF_REF_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The number of ref basecalls observed at sites where the genome reference == C.
calculateDerivedFields() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
 
calculateDerivedMetrics() - Method in class picard.sam.DuplicationMetrics
Fills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where possible and the PERCENT_DUPLICATION.
calculateDerivedStatistics() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
Calculate the error rate given the raw counts.
calculateDerivedStatistics() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
Calculate the error rate given the raw counts.
calculateGenotypeConcordance(GenotypeConcordanceScheme, boolean) - Method in class picard.vcf.GenotypeConcordanceCounts
Genotype Concordance is the number of times the truth and call states match exactly / all truth and call combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
CalculateHsMetrics - Class in picard.analysis.directed
Calculates a set of HS metrics from a sam or bam file.
CalculateHsMetrics() - Constructor for class picard.analysis.directed.CalculateHsMetrics
 
calculateNonRefGenotypeConcordance(GenotypeConcordanceScheme, boolean) - Method in class picard.vcf.GenotypeConcordanceCounts
Non Ref Genotype Concordance is the number of times the truth and call states match exactly for *vars only* / all truth and call *var* combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
CalculateReadGroupChecksum - Class in picard.sam
 
CalculateReadGroupChecksum() - Constructor for class picard.sam.CalculateReadGroupChecksum
 
calculateRoiHistogram() - Method in class picard.sam.DuplicationMetrics
Calculates a histogram using the estimateRoi method to estimate the effective yield doing x sequencing for x=1..10.
calculateWordCount(byte[]) - Method in class picard.util.AbstractInputParser
Calculates the number of delimiter-separated "words" in a line and sets the value of wordCount
CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordance
 
CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The name of the 'call' sample
CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The name of the 'call' sample
CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The name of the 'call' sample
CALL_STATE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The state of the 'call' sample (i.e.
CALL_VCF - Variable in class picard.vcf.GenotypeConcordance
 
CallingMetricAccumulator - Class in picard.vcf
Collects variants and generates metrics about them.
CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets) - Constructor for class picard.vcf.CallingMetricAccumulator
 
CallingMetricAccumulator.Result - Class in picard.vcf
 
canSkip() - Method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
 
canSkipSAMFile(File, int, boolean, File) - Static method in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
Checks if we can skip the SAM/BAM file when reverting origin base qualities and adding mate cigars.
Casava18ReadNameEncoder - Class in picard.fastq
A read name encoder conforming to the standard described by Illumina Casava 1.8.
Casava18ReadNameEncoder(String, String, String) - Constructor for class picard.fastq.Casava18ReadNameEncoder
 
CATEGORY - Variable in class picard.analysis.AlignmentSummaryMetrics
One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregated for both first and second reads in a pair.
CHAIN - Variable in class picard.util.LiftOverIntervalList
 
CHAIN - Variable in class picard.vcf.LiftoverVcf
 
CHART_OUTPUT - Variable in class picard.analysis.CollectBaseDistributionByCycle
 
CHART_OUTPUT - Variable in class picard.analysis.CollectGcBiasMetrics
 
CHART_OUTPUT - Variable in class picard.analysis.CollectRnaSeqMetrics
 
CHART_OUTPUT - Variable in class picard.analysis.MeanQualityByCycle
 
CHART_OUTPUT - Variable in class picard.analysis.QualityScoreDistribution
 
CheckIlluminaDirectory - Class in picard.illumina
Program to check a lane of an Illumina output directory.
CheckIlluminaDirectory() - Constructor for class picard.illumina.CheckIlluminaDirectory
 
CheckTerminatorBlock - Class in picard.sam
Simple class to check the terminator block of a SAM file.
CheckTerminatorBlock() - Constructor for class picard.sam.CheckTerminatorBlock
 
CHIMERA_KB_MIN - Variable in class picard.analysis.CollectJumpingLibraryMetrics
 
CHIMERIC_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of pairs where either (a) the ends fall on different chromosomes or (b) the insert size is greater than the maximum of 100000 or 2 times the mode of the insert size for outward-facing pairs.
CircularByteBuffer - Class in picard.util
Implementation of a circular byte buffer that uses a large byte[] internally and supports basic read/write operations from/to other byte[]s passed as arguments.
CircularByteBuffer(int) - Constructor for class picard.util.CircularByteBuffer
Constructs a buffer capable of holding the given number of bytes.
ClassFinder - Class in picard.cmdline
Utility class that can scan for classes in the classpath and find all the ones annotated with a particular annotation.
ClassFinder() - Constructor for class picard.cmdline.ClassFinder
 
ClassFinder(ClassLoader) - Constructor for class picard.cmdline.ClassFinder
 
ClassFinder(File) - Constructor for class picard.cmdline.ClassFinder
 
CLASSIFICATION - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
The classification of this read: {EMPTY, POLYCLONAL, MISALIGNED, UNKNOWN} (See PFFailSummaryMetric for explanation regarding the possible classification.)
CleanSam - Class in picard.sam
 
CleanSam() - Constructor for class picard.sam.CleanSam
 
CLIP_ADAPTERS - Variable in class picard.fastq.BamToBfq
 
CLIP_ADAPTERS - Variable in class picard.sam.MergeBamAlignment
 
CLIP_OVERLAPPING_READS - Variable in class picard.sam.MergeBamAlignment
 
clipForOverlappingReads(SAMRecord, SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
Checks to see whether the ends of the reads overlap and soft clips reads them if necessary.
CLIPPING_ACTION - Variable in class picard.sam.SamToFastq
 
CLIPPING_ATTRIBUTE - Variable in class picard.sam.SamToFastq
 
ClippingUtility - Class in picard.util
Utilities to clip the adapater sequence from a SAMRecord read
ClippingUtility() - Constructor for class picard.util.ClippingUtility
 
ClocsFileFaker - Class in picard.illumina.parser.fakers
 
ClocsFileFaker() - Constructor for class picard.illumina.parser.fakers.ClocsFileFaker
 
ClocsFileReader - Class in picard.illumina.parser.readers
The clocs file format is one of 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
ClocsFileReader(File) - Constructor for class picard.illumina.parser.readers.ClocsFileReader
 
clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
close() - Method in interface picard.illumina.IlluminaBasecallsConverter.ConvertedClusterDataWriter
 
close() - Method in class picard.illumina.parser.IlluminaDataProvider
 
close() - Method in class picard.illumina.parser.MultiTileFilterParser
 
close() - Method in class picard.illumina.parser.MultiTileLocsParser
 
close() - Method in class picard.illumina.parser.PerTileParser
 
close() - Method in class picard.illumina.parser.readers.BarcodeFileReader
 
close() - Method in class picard.illumina.parser.readers.BclReader
 
close() - Method in class picard.illumina.parser.readers.ClocsFileReader
 
close() - Method in class picard.illumina.parser.readers.LocsFileReader
 
close() - Method in class picard.illumina.parser.readers.PosFileReader
 
close() - Method in class picard.sam.AbstractAlignmentMerger
 
close() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
close() - Method in class picard.util.AbstractInputParser
Closes this stream and releases any system resources associated with it.
close() - Method in class picard.util.AsyncIterator
Stops the thread and then calls synchronouslyClose() to allow implementation to do any one time clean up.
close() - Method in class picard.util.BasicInputParser
Closes the underlying stream
close() - Method in class picard.util.CircularByteBuffer
Signals that the buffer is closed and no further writes will occur.
close() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
close() - Method in class picard.util.TabbedTextFileWithHeaderParser
Release all resources associated with the parser.
close() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
 
close() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
 
close() - Method in class picard.vcf.processor.VariantIteratorProducer
Closes any latent file handles that may have been opened by calls to VariantIteratorProducer.iterators().
closeWriter() - Method in class picard.sam.FixMateInformation
 
CLUSTER_DENSITY - Variable in class picard.illumina.IlluminaLaneMetrics
The number of clusters per unit area on the this lane expressed in units of [cluster / mm^2].
ClusterData - Class in picard.illumina.parser
Store the information from Illumina files for a single cluster with one or more reads.
ClusterData(ReadData...) - Constructor for class picard.illumina.parser.ClusterData
Used for testing, reads is set directly with no copying to the input array
ClusterData(ReadType[]) - Constructor for class picard.illumina.parser.ClusterData
Creates a ClusterData with one read for each type provided
ClusterDataToSamConverter - Class in picard.illumina
Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords, as appropriate, and optionally marking adapter sequence.
ClusterDataToSamConverter(String, String, ReadStructure, List<IlluminaUtil.IlluminaAdapterPair>) - Constructor for class picard.illumina.ClusterDataToSamConverter
Constructor
CODING_BASES - Variable in class picard.analysis.RnaSeqMetrics
Number of bases in primary aligments that align to a non-UTR coding base for some gene, and not ribosomal sequence.
codingEnd - Variable in class picard.annotation.Gene.Transcript
 
codingStart - Variable in class picard.annotation.Gene.Transcript
 
CollectAlignmentSummaryMetrics - Class in picard.analysis
A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.
CollectAlignmentSummaryMetrics() - Constructor for class picard.analysis.CollectAlignmentSummaryMetrics
 
CollectBaseDistributionByCycle - Class in picard.analysis
 
CollectBaseDistributionByCycle() - Constructor for class picard.analysis.CollectBaseDistributionByCycle
 
CollectGcBiasMetrics - Class in picard.analysis
Tool to collect information about GC bias in the reads in a given BAM file.
CollectGcBiasMetrics() - Constructor for class picard.analysis.CollectGcBiasMetrics
 
CollectHiSeqXPfFailMetrics - Class in picard.illumina.quality
Collect metrics regarding the reason for reads (sequenced by HiSeqX) not passing the Illumina PF Filter.
CollectHiSeqXPfFailMetrics() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
CollectHiSeqXPfFailMetrics.PFFailDetailedMetric - Class in picard.illumina.quality
a metric class for describing FP failing reads from an Illumina HiSeqX lane *
CollectHiSeqXPfFailMetrics.PFFailDetailedMetric(Integer, int, int, int, int, CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
 
CollectHiSeqXPfFailMetrics.PFFailDetailedMetric() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
This ctor is necessary for when reading metrics from file
CollectHiSeqXPfFailMetrics.PFFailSummaryMetric - Class in picard.illumina.quality
Metrics produced by the GetHiSeqXPFFailMetrics program.
CollectHiSeqXPfFailMetrics.PFFailSummaryMetric(String) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
 
CollectHiSeqXPfFailMetrics.PFFailSummaryMetric() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
This ctor is necessary for when reading metrics from file
CollectHiSeqXPfFailMetrics.ReadClassifier - Class in picard.illumina.quality
 
CollectHiSeqXPfFailMetrics.ReadClassifier(ReadData) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier
Heart of CLP.
CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason - Enum in picard.illumina.quality
 
CollectIlluminaBasecallingMetrics - Class in picard.illumina
A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect.
CollectIlluminaBasecallingMetrics() - Constructor for class picard.illumina.CollectIlluminaBasecallingMetrics
 
CollectIlluminaLaneMetrics - Class in picard.illumina
CollectIlluminaLaneMetrics() - Constructor for class picard.illumina.CollectIlluminaLaneMetrics
 
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector - Class in picard.illumina
Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector() - Constructor for class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
 
CollectInsertSizeMetrics - Class in picard.analysis
Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.
CollectInsertSizeMetrics() - Constructor for class picard.analysis.CollectInsertSizeMetrics
 
CollectJumpingLibraryMetrics - Class in picard.analysis
Command-line program to compute metrics about outward-facing pairs, inward-facing pairs, and chimeras in a jumping library.
CollectJumpingLibraryMetrics() - Constructor for class picard.analysis.CollectJumpingLibraryMetrics
 
collectLaneMetrics(File, File, String, MetricsFile<MetricBase, Comparable<?>>, MetricsFile<MetricBase, Comparable<?>>, ReadStructure) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files
CollectMultipleMetrics - Class in picard.analysis
Class that is designed to instantiate and execute multiple metrics programs that extend SinglePassSamProgram while making only a single pass through the SAM file and supplying each program with the records as it goes.
CollectMultipleMetrics() - Constructor for class picard.analysis.CollectMultipleMetrics
 
CollectMultipleMetrics.Program - Enum in picard.analysis
 
CollectMultipleMetrics.ProgramInterface - Interface in picard.analysis
This interface allows developers to create Programs to run in addition to the ones defined in the Program enum.
CollectOxoGMetrics - Class in picard.analysis
Class for trying to quantify the CpCG->CpCA error rate.
CollectOxoGMetrics() - Constructor for class picard.analysis.CollectOxoGMetrics
 
CollectOxoGMetrics.CpcgMetrics - Class in picard.analysis
Metrics class for outputs.
CollectOxoGMetrics.CpcgMetrics() - Constructor for class picard.analysis.CollectOxoGMetrics.CpcgMetrics
 
CollectQualityYieldMetrics - Class in picard.analysis
Command line program to calibrate quality yield metrics
CollectQualityYieldMetrics() - Constructor for class picard.analysis.CollectQualityYieldMetrics
 
CollectQualityYieldMetrics.QualityYieldMetrics - Class in picard.analysis
A set of metrics used to describe the general quality of a BAM file
CollectQualityYieldMetrics.QualityYieldMetrics() - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
 
CollectRawWgsMetrics - Class in picard.analysis
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments, same implementation as CollectWgsMetrics, with different defaults: lacks baseQ and mappingQ filters and has much higher coverage cap.
CollectRawWgsMetrics() - Constructor for class picard.analysis.CollectRawWgsMetrics
 
CollectRawWgsMetrics.RawWgsMetrics - Class in picard.analysis
 
CollectRawWgsMetrics.RawWgsMetrics() - Constructor for class picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
 
CollectRnaSeqMetrics - Class in picard.analysis
 
CollectRnaSeqMetrics() - Constructor for class picard.analysis.CollectRnaSeqMetrics
 
CollectRrbsMetrics - Class in picard.analysis
Calculates and reports QC metrics for RRBS data based on the methylation status at individual C/G bases as well as CpG sites across all reads in the input BAM/SAM file.
CollectRrbsMetrics() - Constructor for class picard.analysis.CollectRrbsMetrics
 
CollectSequencingArtifactMetrics - Class in picard.analysis.artifacts
Quantify substitution errors caused by mismatched base pairings during various stages of sample / library prep.
CollectSequencingArtifactMetrics() - Constructor for class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
CollectTargetedMetrics<METRIC extends MultilevelMetrics,COLLECTOR extends TargetMetricsCollector<METRIC>> - Class in picard.analysis.directed
Both CollectTargetedPCRMetrics and CalculateHybridSelection metrics share virtually identical program structures except for the name of their targeting mechanisms (e.g.
CollectTargetedMetrics() - Constructor for class picard.analysis.directed.CollectTargetedMetrics
 
CollectTargetedPcrMetrics - Class in picard.analysis.directed
Collect metric information for target pcr metrics runs.
CollectTargetedPcrMetrics() - Constructor for class picard.analysis.directed.CollectTargetedPcrMetrics
 
CollectVariantCallingMetrics - Class in picard.vcf
Collects summary and per-sample metrics about variant calls in a VCF file.
CollectVariantCallingMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics
 
CollectVariantCallingMetrics.VariantCallingDetailMetrics - Class in picard.vcf
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
CollectVariantCallingMetrics.VariantCallingDetailMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
 
CollectVariantCallingMetrics.VariantCallingSummaryMetrics - Class in picard.vcf
A collection of metrics relating to snps and indels within a variant-calling file (VCF).
CollectVariantCallingMetrics.VariantCallingSummaryMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
 
CollectWgsMetrics - Class in picard.analysis
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
CollectWgsMetrics() - Constructor for class picard.analysis.CollectWgsMetrics
 
CollectWgsMetrics.WgsMetrics - Class in picard.analysis
Metrics for evaluating the performance of whole genome sequencing experiments.
CollectWgsMetrics.WgsMetrics() - Constructor for class picard.analysis.CollectWgsMetrics.WgsMetrics
 
COLOR_STATUS - Static variable in class picard.cmdline.CommandLineDefaults
Implementation note, this is duplicate code stolen from HTSJDK's Default.java /** Decides if we want to write colors to the terminal.
columnLabels() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
columnLabels() - Method in class picard.util.TabbedTextFileWithHeaderParser
 
combiningResultsBy(VariantProcessor.ResultMerger<R>) - Method in class picard.vcf.processor.VariantProcessor.Builder
 
CommandLineDefaults - Class in picard.cmdline
Embodies defaults for global values that affect how the Picard Command Line operates.
CommandLineDefaults() - Constructor for class picard.cmdline.CommandLineDefaults
 
CommandLineParseException - Exception in picard.cmdline
 
CommandLineParseException(String) - Constructor for exception picard.cmdline.CommandLineParseException
 
CommandLineParseException(String, Throwable) - Constructor for exception picard.cmdline.CommandLineParseException
 
CommandLineParser - Class in picard.cmdline
Annotation-driven utility for parsing command-line arguments, checking for errors, and producing usage message.
CommandLineParser(Object) - Constructor for class picard.cmdline.CommandLineParser
Prepare for parsing command line arguments, by validating annotations.
CommandLineParser.ClpEnum - Interface in picard.cmdline
 
CommandLineParser.OptionDefinition - Class in picard.cmdline
 
CommandLineParserDefinitionException - Exception in picard.cmdline
 
CommandLineParserDefinitionException(String) - Constructor for exception picard.cmdline.CommandLineParserDefinitionException
 
CommandLineParserDefinitionException(String, Throwable) - Constructor for exception picard.cmdline.CommandLineParserDefinitionException
 
CommandLineProgram - Class in picard.cmdline
Abstract class to facilitate writing command-line programs.
CommandLineProgram() - Constructor for class picard.cmdline.CommandLineProgram
 
CommandLineProgramGroup - Interface in picard.cmdline
Interface for groups of CommandLinePrograms.
CommandLineProgramProperties - Annotation Type in picard.cmdline
Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
COMMENT - Variable in class picard.sam.AddCommentsToBam
 
COMMENT - Variable in class picard.sam.FastqToSam
 
COMMENT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
COMMENT - Variable in class picard.sam.MergeSamFiles
 
COMMENT - Variable in class picard.util.IntervalListTools
 
comparator - Static variable in interface picard.cmdline.CommandLineProgramGroup
Compares two program groups by name.
compare(int, int) - Static method in class picard.util.MathUtil
 
compareDoubleWithAccuracy(double, double, double) - Static method in class picard.util.TestNGUtil
Small utility function for determining if two doubles are within a _relative_ accuracy of each other.
CompareMetrics - Class in picard.analysis
Compare two metrics files.
CompareMetrics() - Constructor for class picard.analysis.CompareMetrics
 
CompareSAMs - Class in picard.sam
Rudimentary SAM comparer.
CompareSAMs() - Constructor for class picard.sam.CompareSAMs
 
compareTo(Gene) - Method in class picard.annotation.Gene
 
COMPRESS_OUTPUTS - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
COMPRESS_OUTPUTS - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
COMPRESSION_LEVEL - Variable in class picard.cmdline.CommandLineProgram
 
CON_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact.
CON_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact.
CONTEXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The sequence context to which the analysis is constrained.
CONTEXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The sequence context to which the analysis is constrained.
CONTEXT - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The sequence context being reported on.
CONTEXT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
CONTEXT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
 
CONTEXTS - Variable in class picard.analysis.CollectOxoGMetrics
 
CONTEXTS_TO_PRINT - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
contig() - Method in class picard.vcf.processor.VcfFileSegment
 
CONTINGENCY_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
 
CONTINGENCY_VALUES - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The list of contingency table values (TP, TN, FP, FN) that are deduced from the truth/call state comparison, given the reference.
convertClusterToOutputRecord(ClusterData) - Method in class picard.illumina.ClusterDataToSamConverter
Creates the SAMRecord for each read in the cluster
convertClusterToOutputRecord(ClusterData) - Method in interface picard.illumina.IlluminaBasecallsConverter.ClusterDataConverter
Creates the OUTPUT_RECORDs from the cluster
CONVERTED_SITES - Variable in class picard.analysis.RrbsCpgDetailMetrics
Number of times this CpG site was converted (TG for + strand, CA for - strand)
convertMetric(TargetMetrics) - Method in class picard.analysis.directed.HsMetricCollector
 
convertMetric(TargetMetrics) - Method in class picard.analysis.directed.TargetedPcrMetricsCollector
 
convertMetric(TargetMetrics) - Method in class picard.analysis.directed.TargetMetricsCollector
 
ConvertSequencingArtifactToOxoG - Class in picard.analysis.artifacts
 
ConvertSequencingArtifactToOxoG() - Constructor for class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 
convertSolexaQualityAscii_1_1_ToPhredBinary(byte[]) - Static method in class picard.util.IlluminaUtil
Converts from Solexa ASCII to Phred binary in place.
copy(ExtractIlluminaBarcodes.BarcodeMetric) - Static method in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
Creates a copy of metric initialized with only non-accumulated and non-calculated values set
CORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
Number of aligned reads that map to the correct strand.
correspondingInterval() - Method in class picard.vcf.processor.VcfFileSegment
 
COUNT - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The number of events of type TRUTH_STATE and CALL_STATE for the EVENT_TYPE and SAMPLEs
COVERAGE_CAP - Variable in class picard.analysis.CollectRawWgsMetrics
 
COVERAGE_CAP - Variable in class picard.analysis.CollectWgsMetrics
 
CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
Number of CpG sites that were converted (TG for +, CA for -)
CPG_BASES_SEEN - Variable in class picard.analysis.RrbsSummaryMetrics
Number of CpG sites encountered
CREATE_INDEX - Variable in class picard.cmdline.CommandLineProgram
 
CREATE_MD5_FILE - Variable in class picard.cmdline.CommandLineProgram
 
CreateHtmlDocForProgram - Class in picard.cmdline
Print out the usage for one or more CommandLinePrograms in a form close to what is used in the Sourceforge Picard website.
CreateHtmlDocForProgram() - Constructor for class picard.cmdline.CreateHtmlDocForProgram
 
CreateHtmlDocForStandardOptions - Class in picard.cmdline
 
CreateHtmlDocForStandardOptions() - Constructor for class picard.cmdline.CreateHtmlDocForStandardOptions
 
createNewCigarsIfMapsOffEndOfReference(SAMRecord) - Static method in class picard.sam.AbstractAlignmentMerger
Soft-clip an alignment that hangs off the end of its reference sequence.
createSamFileHeader() - Method in class picard.sam.FastqToSam
Creates a simple header with the values provided on the command line.
createSamFileWriter(SAMFileHeader) - Method in class picard.sam.FixMateInformation
 
CreateSequenceDictionary - Class in picard.sam
Create a SAM/BAM file from a fasta containing reference sequence.
CreateSequenceDictionary() - Constructor for class picard.sam.CreateSequenceDictionary
 
createSnpAndIndelBitSets(File, SAMSequenceDictionary) - Static method in class picard.util.DbSnpBitSetUtil
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
CsvInputParser - Class in picard.util
 
CsvInputParser(boolean, InputStream...) - Constructor for class picard.util.CsvInputParser
Constructor
CsvInputParser(boolean, File...) - Constructor for class picard.util.CsvInputParser
Constructor
CUSTOM_AMPLICON_SET - Variable in class picard.analysis.directed.TargetedPcrMetrics
The name of the amplicon set used in this metrics collection run
CUSTOM_AMPLICON_SET_NAME - Variable in class picard.analysis.directed.CollectTargetedPcrMetrics
 
customCommandLineValidation() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
customCommandLineValidation() - Method in class picard.analysis.CollectInsertSizeMetrics
Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.analysis.CollectMultipleMetrics
 
customCommandLineValidation() - Method in class picard.analysis.CollectOxoGMetrics
 
customCommandLineValidation() - Method in class picard.analysis.CollectRrbsMetrics
 
customCommandLineValidation() - Method in class picard.analysis.directed.CollectTargetedMetrics
 
customCommandLineValidation() - Method in class picard.cmdline.CommandLineProgram
Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.fastq.BamToBfq
 
customCommandLineValidation() - Method in class picard.illumina.CheckIlluminaDirectory
 
customCommandLineValidation() - Method in class picard.illumina.ExtractIlluminaBarcodes
Validate that POSITION >= 1, and that all BARCODEs are the same length and unique
customCommandLineValidation() - Method in class picard.illumina.IlluminaBasecallsToFastq
 
customCommandLineValidation() - Method in class picard.illumina.IlluminaBasecallsToSam
Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.illumina.MarkIlluminaAdapters
 
customCommandLineValidation() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
customCommandLineValidation() - Method in class picard.sam.CreateSequenceDictionary
Use reference filename to create URI to go into header if URI was not passed on cmd line.
customCommandLineValidation() - Method in class picard.sam.FastqToSam
 
customCommandLineValidation() - Method in class picard.sam.FilterSamReads
 
customCommandLineValidation() - Method in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
customCommandLineValidation() - Method in class picard.sam.MergeBamAlignment
Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.sam.MergeSamFiles
 
customCommandLineValidation() - Method in class picard.sam.PositionBasedDownsampleSam
 
customCommandLineValidation() - Method in class picard.sam.RevertSam
Enforce that output ordering is queryname when sanitization is turned on since it requires a queryname sort.
customCommandLineValidation() - Method in class picard.sam.SamToFastq
Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.sam.ViewSam
 
customCommandLineValidation() - Method in class picard.util.BaitDesigner
 
customCommandLineValidation() - Method in class picard.util.IntervalListTools
 
customCommandLineValidation() - Method in class picard.vcf.GenotypeConcordance
 
CYCLE - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
CYCLE_SUBDIRECTORY_PATTERN - Static variable in class picard.illumina.parser.IlluminaFileUtil
 

D

DATA_TYPES - Variable in class picard.illumina.CheckIlluminaDirectory
 
DATA_TYPES_NO_BARCODE - Static variable in class picard.illumina.IlluminaBasecallsConverter
 
dataFile - Variable in class picard.illumina.parser.MultiTileFileUtil
 
DB_SNP - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
DB_SNP - Variable in class picard.analysis.CollectOxoGMetrics
 
DBSNP - Variable in class picard.vcf.CollectVariantCallingMetrics
 
DBSNP_INS_DEL_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The Insertion/Deletion ratio of the Indel calls made at dbSNP sites
DBSNP_TITV - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The Transition/Transversion ratio of the SNP calls made at dbSNP sites
DbSnpBitSetUtil - Class in picard.util
Utility class to use with DbSnp files to determine is a locus is a dbSnp site.
DbSnpBitSetUtil(File, SAMSequenceDictionary) - Constructor for class picard.util.DbSnpBitSetUtil
Constructor that creates a bit set with bits set to true for all variant types.
DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<VariantType>) - Constructor for class picard.util.DbSnpBitSetUtil
Constructor.
DbSnpBitSetUtil.DbSnpBitSets - Class in picard.util
Little tuple class to contain one bitset for SNPs and another for Indels.
DbSnpBitSetUtil.DbSnpBitSets() - Constructor for class picard.util.DbSnpBitSetUtil.DbSnpBitSets
 
DEBUG_FREQUENCY - Variable in class picard.util.FifoBuffer
 
decode() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
DEFAULT_ADAPTER_LENGTH - Static variable in class picard.util.AdapterMarker
 
DEFAULT_NUM_ADAPTERS_TO_KEEP - Static variable in class picard.util.AdapterMarker
 
DEFAULT_OPTICAL_DUPLICATE_DISTANCE - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN - Static variable in class picard.util.AdapterMarker
 
DEFAULT_QUEUE_SIZE - Static variable in class picard.util.AsyncIterator
 
DEFAULT_READ_NAME_REGEX - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
DEFAULT_READ_NAME_REGEX - Static variable in class picard.sam.util.PhysicalLocation
 
DefaultSkipEmptyFiles - Static variable in class picard.illumina.parser.ParameterizedFileUtil
 
DelimitedTextFileWithHeaderIterator - Class in picard.util
Iterate through a delimited text file in which columns are found by looking at a header line rather than by position.
DelimitedTextFileWithHeaderIterator(BasicInputParser) - Constructor for class picard.util.DelimitedTextFileWithHeaderIterator
 
DelimitedTextFileWithHeaderIterator.Row - Class in picard.util
 
DepthFilter - Class in picard.vcf.filter
Filters out a record if all variant samples have depth lower than the given value.
DepthFilter(int) - Constructor for class picard.vcf.filter.DepthFilter
 
DESCRIPTION - Variable in class picard.sam.FastqToSam
 
descriptors - Variable in class picard.illumina.parser.ReadStructure
 
DESIGN_NAME - Variable in class picard.util.BaitDesigner
 
DESIGN_ON_TARGET_STRAND - Variable in class picard.util.BaitDesigner
 
DESIGN_STRATEGY - Variable in class picard.util.BaitDesigner
 
DETAIL_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
 
DETAILED_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
 
detailedMetricsExtension - Static variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
DETAILS - Variable in class picard.metrics.GcBiasMetrics
 
determineFormats(Set<IlluminaDataType>, IlluminaFileUtil) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
For all requestedDataTypes return a map of file format to set of provided data types that covers as many requestedDataTypes as possible and chooses the most preferred available formats possible
determineQualityFormat(FastqReader, FastqReader, FastqQualityFormat) - Static method in class picard.sam.FastqToSam
Looks at fastq input(s) and attempts to determine the proper quality format Closes the reader(s) by side effect
DEVIATIONS - Variable in class picard.analysis.CollectInsertSizeMetrics
 
DiskBasedReadEndsForMarkDuplicatesMap - Class in picard.sam.markduplicates.util
Disk-based implementation of ReadEndsForMarkDuplicatesMap.
DiskBasedReadEndsForMarkDuplicatesMap(int) - Constructor for class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
 
divide(double[], double[]) - Static method in class picard.util.MathUtil
Calculates the ratio of two arrays of the same length.
doBugWorkAround() - Static method in class picard.util.FileChannelJDKBugWorkAround
 
doMetaTest(TestClazz) - Method in class picard.util.TestNGUtil.SingleTestUnitTest
 
doPaired(FastqReader, FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
More complicated method that takes two fastq files and builds pairing information in the SAM.
doTest(TestClazz) - Method in class picard.util.TestNGUtil.SingleTestUnitTest
 
doTileProcessing() - Method in class picard.illumina.IlluminaBasecallsConverter
Do the work, i.e.
doUnpaired(FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
Creates a simple SAM file from a single fastq file.
DownsampleSam - Class in picard.sam
Class to randomly downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither end of the pair!
DownsampleSam() - Constructor for class picard.sam.DownsampleSam
 
doWork() - Method in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 
doWork() - Method in class picard.analysis.CollectJumpingLibraryMetrics
Calculates the detailed statistics about the jumping library and then generates the results.
doWork() - Method in class picard.analysis.CollectMultipleMetrics
 
doWork() - Method in class picard.analysis.CollectOxoGMetrics
 
doWork() - Method in class picard.analysis.CollectQualityYieldMetrics
Main method for the program.
doWork() - Method in class picard.analysis.CollectRrbsMetrics
 
doWork() - Method in class picard.analysis.CollectWgsMetrics
 
doWork() - Method in class picard.analysis.CompareMetrics
 
doWork() - Method in class picard.analysis.directed.CollectTargetedMetrics
Asserts that files are readable and writable and then fires off an HsMetricsCalculator instance to do the real work.
doWork() - Method in class picard.analysis.SinglePassSamProgram
Final implementation of doWork() that checks and loads the input and optionally reference sequence files and the runs the sublcass through the setup() acceptRead() and finish() steps.
doWork() - Method in class picard.cmdline.CommandLineProgram
Do the work after command line has been parsed.
doWork() - Method in class picard.fastq.BamToBfq
 
doWork() - Method in class picard.illumina.CheckIlluminaDirectory
 
doWork() - Method in class picard.illumina.CollectIlluminaBasecallingMetrics
 
doWork() - Method in class picard.illumina.CollectIlluminaLaneMetrics
 
doWork() - Method in class picard.illumina.ExtractIlluminaBarcodes
 
doWork() - Method in class picard.illumina.IlluminaBasecallsToFastq
 
doWork() - Method in class picard.illumina.IlluminaBasecallsToSam
 
doWork() - Method in class picard.illumina.MarkIlluminaAdapters
 
doWork() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
doWork() - Method in class picard.reference.ExtractSequences
 
doWork() - Method in class picard.reference.NormalizeFasta
 
doWork() - Method in class picard.sam.AddCommentsToBam
 
doWork() - Method in class picard.sam.AddOrReplaceReadGroups
 
doWork() - Method in class picard.sam.BamIndexStats
Main method for the program.
doWork() - Method in class picard.sam.BuildBamIndex
Main method for the program.
doWork() - Method in class picard.sam.CalculateReadGroupChecksum
 
doWork() - Method in class picard.sam.CheckTerminatorBlock
 
doWork() - Method in class picard.sam.CleanSam
Do the work after command line has been parsed.
doWork() - Method in class picard.sam.CompareSAMs
Do the work after command line has been parsed.
doWork() - Method in class picard.sam.CreateSequenceDictionary
Do the work after command line has been parsed.
doWork() - Method in class picard.sam.DownsampleSam
 
doWork() - Method in class picard.sam.FastqToSam
 
doWork() - Method in class picard.sam.FilterSamReads
 
doWork() - Method in class picard.sam.FixMateInformation
 
doWork() - Method in class picard.sam.GatherBamFiles
 
doWork() - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
Method that does most of the work.
doWork() - Method in class picard.sam.markduplicates.MarkDuplicates
Main work method.
doWork() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
Main work method.
doWork() - Method in class picard.sam.MergeBamAlignment
 
doWork() - Method in class picard.sam.MergeSamFiles
Combines multiple SAM/BAM files into one.
doWork() - Method in class picard.sam.PositionBasedDownsampleSam
 
doWork() - Method in class picard.sam.ReorderSam
 
doWork() - Method in class picard.sam.ReplaceSamHeader
Do the work after command line has been parsed.
doWork() - Method in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
doWork() - Method in class picard.sam.RevertSam
 
doWork() - Method in class picard.sam.SamFormatConverter
 
doWork() - Method in class picard.sam.SamToFastq
 
doWork() - Method in class picard.sam.SortSam
 
doWork() - Method in class picard.sam.SplitSamByLibrary
 
doWork() - Method in class picard.sam.ValidateSamFile
 
doWork() - Method in class picard.sam.ViewSam
 
doWork() - Method in class picard.util.BaitDesigner
Main method that coordinates the checking of inputs, designing of baits and then the writing out of all necessary files.
doWork() - Method in class picard.util.BedToIntervalList
 
doWork() - Method in class picard.util.FifoBuffer
 
doWork() - Method in class picard.util.IntervalListTools
 
doWork() - Method in class picard.util.LiftOverIntervalList
Do the work after command line has been parsed.
doWork() - Method in class picard.util.ScatterIntervalsByNs
 
doWork() - Method in class picard.vcf.CollectVariantCallingMetrics
 
doWork() - Method in class picard.vcf.filter.FilterVcf
 
doWork() - Method in class picard.vcf.GatherVcfs
 
doWork() - Method in class picard.vcf.GenotypeConcordance
 
doWork() - Method in class picard.vcf.LiftoverVcf
 
doWork() - Method in class picard.vcf.MakeSitesOnlyVcf
 
doWork() - Method in class picard.vcf.MergeVcfs
 
doWork() - Method in class picard.vcf.RenameSampleInVcf
 
doWork() - Method in class picard.vcf.SortVcf
 
doWork() - Method in class picard.vcf.SplitVcfs
 
doWork() - Method in class picard.vcf.UpdateVcfSequenceDictionary
 
doWork() - Method in class picard.vcf.VcfFormatConverter
 
doWork() - Method in class picard.vcf.VcfToIntervalList
 
DUPLICATE_SCORING_STRATEGY - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
DuplicationMetrics - Class in picard.sam
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.
DuplicationMetrics() - Constructor for class picard.sam.DuplicationMetrics
 

E

EarliestFragmentPrimaryAlignmentSelectionStrategy - Class in picard.sam
When it is necessary to pick a primary alignment from a group of alignments for a read, pick the one that maps the earliest base in the read.
EarliestFragmentPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy
 
EMPTY - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
EMPTY_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The empty (no contingency info) count across all variants
encode(ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
end() - Method in class picard.annotation.Gene.Transcript
 
end - Variable in class picard.annotation.Gene.Transcript.Exon
 
end - Variable in class picard.illumina.parser.Range
 
equals(Object) - Method in class picard.annotation.Gene
 
equals(Object) - Method in class picard.annotation.Gene.Transcript
 
equals(Object) - Method in class picard.illumina.parser.FourChannelIntensityData
 
equals(Object) - Method in class picard.illumina.parser.Range
 
equals(Object) - Method in class picard.illumina.parser.ReadDescriptor
 
equals(Object) - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
 
equals(Object) - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
 
equals(Object) - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
equals(Object) - Method in class picard.illumina.parser.ReadStructure
 
equals(Object) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
ERROR_BAR_WIDTH - Variable in class picard.analysis.GcBiasDetailMetrics
The radius of error bars in this bin based on the number of observations made.
ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE).
ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The estimated error rate due to this artifact.
ESTIMATED_LIBRARY_SIZE - Variable in class picard.sam.DuplicationMetrics
The estimated number of unique molecules in the library based on PE duplication.
EstimateLibraryComplexity - Class in picard.sam.markduplicates
Attempts to estimate library complexity from sequence alone.
EstimateLibraryComplexity() - Constructor for class picard.sam.markduplicates.EstimateLibraryComplexity
 
estimateLibrarySize(long, long) - Static method in class picard.sam.DuplicationMetrics
Estimates the size of a library based on the number of paired end molecules observed and the number of unique pairs ovserved.
estimateRoi(long, double, long, long) - Static method in class picard.sam.DuplicationMetrics
Estimates the ROI (return on investment) that one would see if a library was sequenced to x higher coverage than the observed coverage.
excludingNonOverlaps(VcfFileSegmentGenerator, OverlapDetector<T>) - Static method in class picard.vcf.processor.VcfFileSegmentGenerator
Returns a decorated VcfFileSegmentGenerator that filters out VcfFileSegments that have no overlap with the provided OverlapDetector.
executeFromClasspath(String, String...) - Static method in class picard.util.RExecutor
Executes the given R script that is stored in a file on the classpath.
executeFromFile(File, String...) - Static method in class picard.util.RExecutor
Executes the given R script that is stored in a file by a call to Rscript.
exons - Variable in class picard.annotation.Gene.Transcript
 
EXPECTED_INSERT_SIZE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
EXPECTED_ORIENTATIONS - Variable in class picard.sam.MergeBamAlignment
 
EXPECTED_VERSION - Variable in class picard.illumina.parser.readers.FilterFileReader
Expected Version
extension - Variable in class picard.illumina.parser.ParameterizedFileUtil
The file extension for this class, file extension does not have the standard meaning in this instance.
ExtractIlluminaBarcodes - Class in picard.illumina
Determine the barcode for each read in an Illumina lane.
ExtractIlluminaBarcodes() - Constructor for class picard.illumina.ExtractIlluminaBarcodes
 
ExtractIlluminaBarcodes.BarcodeMetric - Class in picard.illumina
Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.
ExtractIlluminaBarcodes.BarcodeMetric(String, String, String, String[]) - Constructor for class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
 
ExtractIlluminaBarcodes.BarcodeMetric() - Constructor for class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
This ctor is necessary for when reading metrics from file
ExtractSequences - Class in picard.reference
Simple command line program that allows sub-sequences represented by an interval list to be extracted from a reference sequence file.
ExtractSequences() - Constructor for class picard.reference.ExtractSequences
 

F

F - Static variable in class picard.sam.markduplicates.util.ReadEnds
 
FAKE_FILES - Variable in class picard.illumina.CheckIlluminaDirectory
 
fakeBciFile(File, List<Integer>) - Method in class picard.illumina.parser.fakers.BciFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BciFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BclFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.ClocsFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.FileFaker
 
fakeFile(File, int, int, String) - Method in class picard.illumina.parser.fakers.FileFaker
 
fakeFile(File, List<Integer>, int, String) - Method in class picard.illumina.parser.fakers.FileFaker
 
fakeFile(File, Integer) - Method in class picard.illumina.parser.fakers.FileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.FilterFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.LocsFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.PosFileFaker
 
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.MultiTileBclFileUtil
 
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.MultiTileFileUtil
 
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.ParameterizedFileUtil
Given the expected tiles/expected cycles for this file type create a set of fake files such that the verification criteria are met.
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.PerTileFileUtil
 
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
 
faker - Variable in class picard.illumina.parser.ParameterizedFileUtil
 
Fasta - Class in picard.cmdline.programgroups
 
Fasta() - Constructor for class picard.cmdline.programgroups.Fasta
 
FASTQ - Variable in class picard.sam.FastqToSam
 
FASTQ - Variable in class picard.sam.SamToFastq
 
FASTQ2 - Variable in class picard.sam.FastqToSam
 
FastqToSam - Class in picard.sam
Converts a fastq file to an unaligned BAM/SAM format.
FastqToSam() - Constructor for class picard.sam.FastqToSam
 
FF - Static variable in class picard.sam.markduplicates.util.ReadEnds
 
FifoBuffer - Class in picard.util
A program that is designed to act as a large memory buffer between processes that are connected with unix pipes where one or more processes either produce or consume their input or output in bursts.
FifoBuffer(InputStream, PrintStream) - Constructor for class picard.util.FifoBuffer
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.
FifoBuffer() - Constructor for class picard.util.FifoBuffer
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.
FileChannelJDKBugWorkAround - Class in picard.util
Work-around for the following bug http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6503430 Call the method in the main thread before launching threads that do memory-mapping.
FileChannelJDKBugWorkAround() - Constructor for class picard.util.FileChannelJDKBugWorkAround
 
FileFaker - Class in picard.illumina.parser.fakers
 
FileFaker() - Constructor for class picard.illumina.parser.fakers.FileFaker
 
filesAvailable() - Method in class picard.illumina.parser.MultiTileBclFileUtil
 
filesAvailable() - Method in class picard.illumina.parser.MultiTileFileUtil
 
filesAvailable() - Method in class picard.illumina.parser.ParameterizedFileUtil
Determine whether or not files are available
filesAvailable() - Method in class picard.illumina.parser.PerTileFileUtil
 
filesAvailable() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
 
fileToTile(String) - Method in class picard.illumina.parser.ParameterizedFileUtil
Returns only lane and tile information as PerTileFt's do not have End information.
FILL_POOLS - Variable in class picard.util.BaitDesigner
 
FILTER - Variable in class picard.sam.FilterSamReads
 
filter(VariantContext) - Method in class picard.vcf.filter.AlleleBalanceFilter
 
filter(VariantContext, Genotype) - Method in class picard.vcf.filter.DepthFilter
 
filter(VariantContext) - Method in class picard.vcf.filter.FisherStrandFilter
 
filter(VariantContext, Genotype) - Method in interface picard.vcf.filter.GenotypeFilter
Test whether or not the genotype should be filtered out.
filter(VariantContext, Genotype) - Method in class picard.vcf.filter.GenotypeQualityFilter
 
filter(VariantContext) - Method in class picard.vcf.filter.QdFilter
 
filter(VariantContext) - Method in interface picard.vcf.filter.VariantFilter
Check to see if the VariantContext should have a filter applied to it.
FILTER_CANNOT_LIFTOVER - Static variable in class picard.vcf.LiftoverVcf
Filter name to use when a target cannot be lifted over.
FILTER_MISMATCHING_REF_ALLELE - Static variable in class picard.vcf.LiftoverVcf
Filter name to use when a target is lifted over, but the reference allele doens't match the new reference.
FILTER_NAME - Static variable in class picard.vcf.filter.QdFilter
 
FilterApplyingVariantIterator - Class in picard.vcf.filter
Iterator that dynamically applies filter strings to VariantContext records supplied by an underlying iterator.
FilterApplyingVariantIterator(Iterator<VariantContext>, Collection<VariantFilter>, Collection<GenotypeFilter>) - Constructor for class picard.vcf.filter.FilterApplyingVariantIterator
Constructs an iterator from an underlying iterator and the provided (possibly empty) collections of variant and genotype filters.
FILTERED_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of indels that are also filtered
FILTERED_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of SNPs that are also filtered
FilterFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
FilterFileFaker() - Constructor for class picard.illumina.parser.fakers.FilterFileFaker
 
FilterFileReader - Class in picard.illumina.parser.readers
Illumina uses an algorithm described in "Theory of RTA" that determines whether or not a cluster passes filter("PF") or not.
FilterFileReader(File) - Constructor for class picard.illumina.parser.readers.FilterFileReader
 
FilterSamReads - Class in picard.sam
From a SAM or BAM file, produce a new SAM or BAM by filtering aligned reads or a list of read names provided in a file (one readname per line)

$Id$

FilterSamReads() - Constructor for class picard.sam.FilterSamReads
 
FilterVcf - Class in picard.vcf.filter
Applies a set of hard filters to Variants and to Genotypes within a VCF.
FilterVcf() - Constructor for class picard.vcf.filter.FilterVcf
Constructor to default to having index creation on.
finalizeAndWriteMetrics(LibraryIdGenerator) - Method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
Writes the metrics given by the libraryIdGenerator to the METRICS_FILE.
find(String, Class<?>) - Method in class picard.cmdline.ClassFinder
Scans the classpath for classes within the specified package and sub-packages that extend the parentType.
findIndexOfClipSequence(byte[], byte[], int, double) - Static method in class picard.util.ClippingUtility
Finds the first index of the adapterSequence sequence in the read sequence requiring at least minMatch bases of pairwise alignment with a maximum number of errors dictated by maxErrorRate.
findOpticalDuplicates(List<? extends OpticalDuplicateFinder.PhysicalLocation>) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
Finds which reads within the list of duplicates are likely to be optical duplicates of one another.
findPreferredFormat(IlluminaDataType, IlluminaFileUtil) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
Given a data type find the most preferred file format even if files are not available
findTile(int) - Method in class picard.illumina.parser.TileIndex
 
findUnmatchedTypes(Set<IlluminaDataType>, Map<IlluminaFileUtil.SupportedIlluminaFormat, Set<IlluminaDataType>>) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
Given a set of formats to data types they provide, find any requested data types that do not have a format associated with them and return them
finish() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
finish() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
 
finish() - Method in class picard.analysis.CollectBaseDistributionByCycle
 
finish() - Method in class picard.analysis.CollectGcBiasMetrics
 
finish() - Method in class picard.analysis.CollectInsertSizeMetrics
 
finish() - Method in class picard.analysis.CollectRnaSeqMetrics
 
finish() - Method in class picard.analysis.directed.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
 
finish() - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
 
finish() - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
 
finish() - Method in class picard.analysis.MeanQualityByCycle
 
finish() - Method in class picard.analysis.QualityScoreDistribution
 
finish() - Method in class picard.analysis.SinglePassSamProgram
Should be implemented by subclasses to do one-time finalization work.
finish() - Method in class picard.metrics.MultiLevelCollector
Call finish on all PerUnitMetricCollectors
finish() - Method in interface picard.metrics.PerUnitMetricCollector
When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
FIRST_TILE - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
FIRST_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
 
firstSentence(Doc) - Static method in class picard.util.MetricsDoclet
Takes a Doc object and uses the firstSentenceTags() to recreate the first sentence text.
FisherStrandFilter - Class in picard.vcf.filter
Filters records based on the phred scaled p-value from the Fisher Strand test stored in the FS attribute.
FisherStrandFilter(double) - Constructor for class picard.vcf.filter.FisherStrandFilter
 
FIVE_PRIME_ADAPTER - Variable in class picard.illumina.MarkIlluminaAdapters
 
FixMateInformation - Class in picard.sam
Class to fix mate pair information for all reads in a SAM file.
FixMateInformation() - Constructor for class picard.sam.FixMateInformation
 
FLOWCELL_BARCODE - Variable in class picard.fastq.BamToBfq
 
FLOWCELL_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
FN_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The FN (false negative) count across all variants
FN_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
FOLD_80_BASE_PENALTY - Variable in class picard.analysis.directed.HsMetrics
The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.
FOLD_80_BASE_PENALTY - Variable in class picard.analysis.directed.TargetedPcrMetrics
The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.
FOLD_ENRICHMENT - Variable in class picard.analysis.directed.HsMetrics
The fold by which the baited region has been amplified above genomic background.
FOLD_ENRICHMENT - Variable in class picard.analysis.directed.TargetedPcrMetrics
The fold by which the amplicon region has been amplified above genomic background.
foldInto(CollectVariantCallingMetrics.VariantCallingDetailMetrics, Collection<CollectVariantCallingMetrics.VariantCallingDetailMetrics>) - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
 
foldInto(T, Collection<T>) - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
 
FORCE_GC - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
FORCE_GC - Variable in class picard.illumina.IlluminaBasecallsToSam
 
formatToDataTypes - Variable in class picard.illumina.parser.IlluminaDataProviderFactory
A Map of file formats to the dataTypes they will provide for this run.
forVcf(File) - Method in class picard.vcf.processor.VcfFileSegmentGenerator
 
FourChannelIntensityData - Class in picard.illumina.parser
Holds a 4 short values for each cycle of a read.
FourChannelIntensityData(int) - Constructor for class picard.illumina.parser.FourChannelIntensityData
 
FP_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The FP (false positive) count across all variants
FP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
FP_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
FP_TN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
FP_TN_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
FR - Static variable in class picard.sam.markduplicates.util.ReadEnds
 
FRACTION - Variable in class picard.sam.PositionBasedDownsampleSam
 
FRAGMENTS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of fragments in the SAM file
fromCode(int) - Static method in enum picard.pedigree.Sex
Decodes the Sex from a numeric code.
fromFile(File, boolean) - Static method in class picard.pedigree.PedFile
Attempts to read a pedigree file into memory.
fromSexMap(Map<String, Sex>) - Static method in class picard.pedigree.PedFile
Function that accepts a map from sample-name to its sex and creates a PEDFile documenting the sexes.
FWD_CXT_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The number of REF_BASE:ALT_BASE alignments at sites with the given reference context.
FWD_CXT_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The number of REF_BASE:REF_BASE alignments at sites with the given reference context.
FWD_ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)).

G

G_REF_ALT_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The number of alt (A/T) basecalls observed at sites where the genome reference == G.
G_REF_OXO_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there were no bias between sites with a C reference base vs.
G_REF_OXO_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
G_REF_REF_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The number of ref basecalls observed at sites where the genome reference == G.
GA4GH_CLIENT_SECRETS - Variable in class picard.cmdline.CommandLineProgram
 
GA4GHScheme - Class in picard.vcf
The scheme is defined in the constructor.
GA4GHScheme() - Constructor for class picard.vcf.GA4GHScheme
 
GA4GHSchemeWithMissingAsHomRef - Class in picard.vcf
The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.
GA4GHSchemeWithMissingAsHomRef() - Constructor for class picard.vcf.GA4GHSchemeWithMissingAsHomRef
 
GatherBamFiles - Class in picard.sam
Program to perform a rapid "gather" operation on BAM files after a scatter operations where the same process has been performed on different regions of a BAM file creating many smaller BAM files that now need to be concatenated back together.
GatherBamFiles() - Constructor for class picard.sam.GatherBamFiles
 
GatherVcfs - Class in picard.vcf
Simple little class that combines multiple VCFs that have exactly the same set of samples and totally discrete sets of loci.
GatherVcfs() - Constructor for class picard.vcf.GatherVcfs
 
GC - Variable in class picard.analysis.GcBiasDetailMetrics
The G+C content of the reference sequence represented by this bin.
GC_DROPOUT - Variable in class picard.analysis.directed.HsMetrics
A measure of how undercovered >= 50% GC regions are relative to the mean.
GC_DROPOUT - Variable in class picard.analysis.directed.TargetedPcrMetrics
A measure of how undercovered >= 50% GC regions are relative to the mean.
GC_DROPOUT - Variable in class picard.analysis.GcBiasSummaryMetrics
Illumina-style GC dropout metric.
GcBiasDetailMetrics - Class in picard.analysis
Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
GcBiasDetailMetrics() - Constructor for class picard.analysis.GcBiasDetailMetrics
 
GcBiasMetrics - Class in picard.metrics
 
GcBiasMetrics() - Constructor for class picard.metrics.GcBiasMetrics
 
GcBiasMetricsCollector - Class in picard.analysis.directed
Calculates GC Bias Metrics on multiple levels Created by kbergin on 3/23/15.
GcBiasMetricsCollector(Set<MetricAccumulationLevel>, Map<String, byte[]>, int[], List<SAMReadGroupRecord>, int, boolean) - Constructor for class picard.analysis.directed.GcBiasMetricsCollector
 
GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector - Class in picard.analysis.directed
 
GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector(String, String, String) - Constructor for class picard.analysis.directed.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
 
GcBiasSummaryMetrics - Class in picard.analysis
High level metrics that capture how biased the coverage in a certain lane is.
GcBiasSummaryMetrics() - Constructor for class picard.analysis.GcBiasSummaryMetrics
 
Gene - Class in picard.annotation
Holds annotation of a gene for storage in an OverlapDetector.
Gene(String, int, int, boolean, String) - Constructor for class picard.annotation.Gene
 
Gene.Transcript - Class in picard.annotation
A single transcript of a gene.
Gene.Transcript(String, int, int, int, int, int) - Constructor for class picard.annotation.Gene.Transcript
 
Gene.Transcript.Exon - Class in picard.annotation
1-based, inclusive representation of an exon.
Gene.Transcript.Exon(int, int) - Constructor for class picard.annotation.Gene.Transcript.Exon
 
GeneAnnotationReader - Class in picard.annotation
Load gene annotations into an OverlapDetector of Gene objects.
GeneAnnotationReader() - Constructor for class picard.annotation.GeneAnnotationReader
 
generateDataProvider(TestNGUtil.TestNGParameterizable[]) - Static method in class picard.util.TestNGUtil
 
generateDataProvider(Iterable<? extends TestNGUtil.TestNGParameterizable>) - Static method in class picard.util.TestNGUtil
 
generateReadName(ClusterData, Integer) - Method in class picard.fastq.Casava18ReadNameEncoder
 
generateReadName(ClusterData, Integer) - Method in class picard.fastq.IlluminaReadNameEncoder
 
generateReadName(ClusterData, Integer) - Method in interface picard.fastq.ReadNameEncoder
Generates a read name string for the provided cluster.
generateWgsMetrics() - Method in class picard.analysis.CollectRawWgsMetrics
 
generateWgsMetrics() - Method in class picard.analysis.CollectWgsMetrics
 
generatingAccumulatorsBy(VariantProcessor.AccumulatorGenerator<A, R>) - Static method in class picard.vcf.processor.VariantProcessor.Builder
 
GENOME_ASSEMBLY - Variable in class picard.sam.CreateSequenceDictionary
 
GENOME_SIZE - Variable in class picard.analysis.directed.HsMetrics
The number of bases in the reference genome used for alignment.
GENOME_SIZE - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of bases in the reference genome used for alignment.
GENOME_TERRITORY - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The number of non-N bases in the genome reference over which coverage will be evaluated.
GENOTYPE_CONCORDANCE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The genotype concordance for all possible states.
GenotypeConcordance - Class in picard.vcf
Calculates the concordance between genotype data for two samples in two different VCFs - one being considered the truth (or reference) the other being the call.
GenotypeConcordance() - Constructor for class picard.vcf.GenotypeConcordance
 
GenotypeConcordanceContingencyMetrics - Class in picard.vcf
Class that holds metrics about the Genotype Concordance contingency tables.
GenotypeConcordanceContingencyMetrics() - Constructor for class picard.vcf.GenotypeConcordanceContingencyMetrics
Empty constructor - needed for unit tests
GenotypeConcordanceCounts - Class in picard.vcf
A class to store the counts for various truth and call state classifications relative to a reference.
GenotypeConcordanceCounts() - Constructor for class picard.vcf.GenotypeConcordanceCounts
 
GenotypeConcordanceDetailMetrics - Class in picard.vcf
Class that holds detail metrics about Genotype Concordance
GenotypeConcordanceDetailMetrics() - Constructor for class picard.vcf.GenotypeConcordanceDetailMetrics
 
GenotypeConcordanceScheme - Class in picard.vcf
This defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.
GenotypeConcordanceScheme() - Constructor for class picard.vcf.GenotypeConcordanceScheme
 
GenotypeConcordanceSchemeFactory - Class in picard.vcf
Created by kbergin on 6/19/15.
GenotypeConcordanceSchemeFactory() - Constructor for class picard.vcf.GenotypeConcordanceSchemeFactory
 
GenotypeConcordanceStateCodes - Enum in picard.vcf
Created by kbergin on 7/30/15.
GenotypeConcordanceStates - Class in picard.vcf
A class to store the various classifications for: 1.
GenotypeConcordanceStates() - Constructor for class picard.vcf.GenotypeConcordanceStates
 
GenotypeConcordanceStates.TruthState - Enum in picard.vcf
These states represent the relationship between a truth genotype and the reference sequence.
GenotypeConcordanceSummaryMetrics - Class in picard.vcf
Class that holds summary metrics about Genotype Concordance
GenotypeConcordanceSummaryMetrics() - Constructor for class picard.vcf.GenotypeConcordanceSummaryMetrics
Empty constructor - needed for unit tests
GenotypeFilter - Interface in picard.vcf.filter
An interface for classes that perform Genotype filtration.
GenotypeQualityFilter - Class in picard.vcf.filter
Genotype filter that filters out genotypes below a given quality threshold.
GenotypeQualityFilter(int) - Constructor for class picard.vcf.filter.GenotypeQualityFilter
 
get(int) - Method in class picard.illumina.parser.readers.BclIndexReader
 
get(int) - Method in class picard.illumina.parser.ReadStructure.Substructure
 
get3PrimeAdapter() - Method in interface picard.util.AdapterPair
 
get3PrimeAdapter() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get3PrimeAdapterBytes() - Method in interface picard.util.AdapterPair
 
get3PrimeAdapterBytes() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get3PrimeAdapterBytesInReadOrder() - Method in interface picard.util.AdapterPair
 
get3PrimeAdapterBytesInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get3PrimeAdapterInReadOrder() - Method in interface picard.util.AdapterPair
 
get3PrimeAdapterInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get5PrimeAdapter() - Method in interface picard.util.AdapterPair
 
get5PrimeAdapter() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get5PrimeAdapterBytes() - Method in interface picard.util.AdapterPair
 
get5PrimeAdapterBytes() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get5PrimeAdapterBytesInReadOrder() - Method in interface picard.util.AdapterPair
 
get5PrimeAdapterBytesInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get5PrimeAdapterInReadOrder() - Method in interface picard.util.AdapterPair
 
get5PrimeAdapterInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
getA() - Method in class picard.illumina.parser.FourChannelIntensityData
 
getActualTiles(List<IlluminaFileUtil.SupportedIlluminaFormat>) - Method in class picard.illumina.parser.IlluminaFileUtil
Get the available tiles for the given formats, if the formats have tile lists that differ then throw an exception, if any of the format
getAllReadsCollector() - Method in class picard.metrics.MultiLevelCollector
Get the PerUnitMetricCollector that collects reads for all levels
getArgv() - Method in class picard.cmdline.CommandLineParser
 
getAvailableTiles() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
Return the list of tiles available for this flowcell and lane.
getBases() - Method in class picard.illumina.parser.BclData
 
getBases() - Method in class picard.illumina.parser.ReadData
 
getBciFile() - Method in class picard.illumina.parser.readers.BclIndexReader
 
getByteBufferIterator(int, int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
 
getByteIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
 
getBytesAvailableToRead() - Method in class picard.util.CircularByteBuffer
Returns the number of bytes that are in the buffer at the time of the method invocation.
getC() - Method in class picard.illumina.parser.FourChannelIntensityData
 
getCallerOptions() - Method in class picard.cmdline.CommandLineParser
 
getCapacity() - Method in class picard.util.CircularByteBuffer
Returns the total capacity of the buffer (empty+filled).
getChainedPgIds(SAMFileHeader) - Method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
We have to re-chain the program groups based on this algorithm.
getChannel(IntensityChannel) - Method in class picard.illumina.parser.FourChannelIntensityData
 
getClasses() - Method in class picard.cmdline.ClassFinder
Fetches the set of classes discovered so far.
getClusterCount() - Method in class picard.illumina.parser.Tile
Returns the number of on this tile.
getClusterDensity() - Method in class picard.illumina.parser.Tile
Returns the cluster density of this tile, in units of [cluster/mm^2].
getCode() - Method in enum picard.vcf.GenotypeConcordanceStates.TruthState
 
getColumnNames() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
getColumnNames() - Method in class picard.util.TabbedTextFileWithHeaderParser
 
getCommandLine() - Method in class picard.cmdline.CommandLineParser
The commandline used to run this program, including any default args that weren't necessarily specified.
getCommandLine() - Method in class picard.cmdline.CommandLineProgram
 
getCommandLineParser() - Method in class picard.cmdline.CommandLineProgram
 
getConcordanceStateArray(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceScheme
Get the concordance state array associate with the given truth state and call state tuple.
getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceScheme
Get the concordance state array associate with the given truth state and call state tuple.
getContingencyStateCounts(GenotypeConcordanceScheme) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the total number of times each contingency state is encountered, summed across all truth/call state pairs.
getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[]) - Method in class picard.vcf.GenotypeConcordanceScheme
Get the contingency state array as a set
getContingencyStateString(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceScheme
Get the contingency state array as a parse-able string
getCount(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the count defined by the truth state set and call state set.
getCount(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the count defined by the truth state set and call state set.
getCounterSize() - Method in class picard.vcf.GenotypeConcordanceCounts
 
getCurrentLine() - Method in class picard.util.BasicInputParser
Provides access to the current (just parsed) line in pre-parsed format.
getCurrentLine() - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
 
getCurrentLine() - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
 
getCurrentLineNumber() - Method in class picard.util.BasicInputParser
NOTE: Because AbstractInputParser pre-fetches the next line, this method actually returns the next line, not the most recent line returned by next().
getCurrentLineNumber() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
getCurrentLineNumber() - Method in class picard.util.TabbedTextFileWithHeaderParser
 
getCycleIndexRanges() - Method in class picard.illumina.parser.OutputMapping
 
getCycleIndexRanges() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
getCycles() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
getDefaultHeaders() - Method in class picard.cmdline.CommandLineProgram
 
getDepths() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
Gets the coverage depths as an array of shorts.
getDescription() - Method in interface picard.cmdline.CommandLineProgramGroup
Gets the description of this program.
getDescription() - Method in class picard.cmdline.programgroups.Fasta
 
getDescription() - Method in class picard.cmdline.programgroups.Illumina
 
getDescription() - Method in class picard.cmdline.programgroups.Intervals
 
getDescription() - Method in class picard.cmdline.programgroups.Metrics
 
getDescription() - Method in class picard.cmdline.programgroups.None
 
getDescription() - Method in class picard.cmdline.programgroups.SamOrBam
 
getDescription() - Method in class picard.cmdline.programgroups.Testing
 
getDescription() - Method in class picard.cmdline.programgroups.VcfOrBcf
 
getDescriptorLengths() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
getDetectedCycles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
 
getExpectedTiles() - Method in class picard.illumina.parser.IlluminaFileUtil
Return the list of tiles we would expect for this lane based on the metrics found in InterOp/TileMetricsOut.bin
getExtension() - Static method in class picard.illumina.IlluminaLaneMetrics
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
getExtension() - Static method in class picard.illumina.IlluminaPhasingMetrics
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
getFactory() - Method in class picard.illumina.IlluminaBasecallsConverter
In case caller needs to get some info from factory.
getFamilyId() - Method in class picard.pedigree.PedFile.PedTrio
 
getFaqLink() - Static method in class picard.cmdline.CommandLineParser
 
getField(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
 
getField(String) - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
 
getFields() - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
 
getFields() - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
 
getFile() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
 
getFile() - Method in class picard.illumina.parser.TileIndex
 
getFileExtension() - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
 
getFileExtension() - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
 
getFileName() - Method in class picard.util.AbstractInputParser
 
getFileName() - Method in class picard.util.BasicInputParser
Gets the name of the file being parsed
getFiles(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclFileUtil
 
getFiles() - Method in class picard.illumina.parser.PerTileFileUtil
 
getFiles(List<Integer>) - Method in class picard.illumina.parser.PerTileFileUtil
 
getFiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
 
getFiles(List<Integer>) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
 
getFiles(int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in.
getFiles(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the original CycleIlluminaFileMap, created on util instantiation, doesn't contain any of these tiles/cycles).
getFloatIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
 
getForceSort() - Method in class picard.sam.SamAlignmentMerger
 
getG() - Method in class picard.illumina.parser.FourChannelIntensityData
 
getGene() - Method in class picard.annotation.Gene.Transcript
 
getHeader() - Method in class picard.sam.AbstractAlignmentMerger
 
getHelpDoc() - Method in interface picard.cmdline.CommandLineParser.ClpEnum
 
getHelpDoc() - Method in enum picard.util.IntervalListTools.Action
 
getHom(int) - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
 
getIndelCounter() - Method in class picard.vcf.GenotypeConcordance
 
getIndices() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
getIndividualId() - Method in class picard.pedigree.PedFile.PedTrio
 
getInputStream() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
getIntegerField(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
 
getIntegerField(String) - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
 
getIntegerIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
 
getLane() - Method in class picard.illumina.parser.ClusterData
 
getLane() - Method in class picard.illumina.parser.IlluminaFileUtil
Return the lane we're inspecting
getLane() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
 
getLaneNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
 
getLaneNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
getLaneNumber() - Method in class picard.illumina.parser.Tile
Returns the number of this tile's parent lane.
getLaneTileCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
getLibraryId(SAMRecord) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
Get the library ID for the given SAM record.
getLibraryId() - Method in interface picard.sam.markduplicates.util.OpticalDuplicateFinder.PhysicalLocation
 
getLibraryId() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
getLibraryId() - Method in class picard.sam.markduplicates.util.ReadEnds
 
getLibraryIdGenerator() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
getLibraryIdsMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getLibraryName(SAMFileHeader, SAMRecord) - Static method in class picard.sam.markduplicates.util.LibraryIdGenerator
Gets the library name from the header for the record.
getLocations(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.MarkQueue
Returns the nonDuplicateReadEndsSet of read ends that should be considered for tracking optical duplicates.
getLocationSet() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
getLog_of_base() - Method in class picard.util.MathUtil.LogMath
 
getLogValue(double) - Method in class picard.util.MathUtil.LogMath
Returns the log-representation of the provided decimal value.
getLogValue(double[]) - Method in class picard.util.MathUtil.LogMath
Returns the log-representation of the provided decimal array.
getLongIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
 
getMappingsDiffer() - Method in class picard.sam.CompareSAMs
 
getMappingsMatch() - Method in class picard.sam.CompareSAMs
 
getMaskedBaseCount(byte[], int, int) - Static method in class picard.util.BaitDesigner
Returns the total of soft or hard masked bases in the interval of bases.
getMatchedBarcode() - Method in class picard.illumina.parser.ClusterData
 
getMaternalId() - Method in class picard.pedigree.PedFile.PedTrio
 
getMaxPairErrorRate() - Method in class picard.util.AdapterMarker
 
getMaxSingleEndErrorRate() - Method in class picard.util.AdapterMarker
 
getMedianPhasingMap() - Method in class picard.illumina.LanePhasingMetricsCollector
 
getMedianPrePhasingMap() - Method in class picard.illumina.LanePhasingMetricsCollector
 
getMessage(int) - Method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
 
getMetricCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
 
getMetricCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
getMetricsByLibrary(String) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getMetricsByLibraryMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getMetricsCode() - Method in enum picard.illumina.parser.IlluminaMetricsCode
 
getMetricsFile() - Method in class picard.cmdline.CommandLineProgram
Gets a MetricsFile with default headers already written into it.
getMetricValue() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
getMinPairMatchBases() - Method in class picard.util.AdapterMarker
 
getMinSingleEndMatchBases() - Method in class picard.util.AdapterMarker
 
getMissingLeft() - Method in class picard.sam.CompareSAMs
 
getMissingRight() - Method in class picard.sam.CompareSAMs
 
getName() - Method in interface picard.cmdline.CommandLineProgramGroup
Gets the name of this program.
getName() - Method in class picard.cmdline.programgroups.Fasta
 
getName() - Method in class picard.cmdline.programgroups.Illumina
 
getName() - Method in class picard.cmdline.programgroups.Intervals
 
getName() - Method in class picard.cmdline.programgroups.Metrics
 
getName() - Method in class picard.cmdline.programgroups.None
 
getName() - Method in class picard.cmdline.programgroups.SamOrBam
 
getName() - Method in class picard.cmdline.programgroups.Testing
 
getName() - Method in class picard.cmdline.programgroups.VcfOrBcf
 
getName() - Method in interface picard.util.AdapterPair
 
getName() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
getNestedOptions() - Method in class picard.cmdline.CommandLineProgram
 
getNestedOptionsForHelp() - Method in class picard.cmdline.CommandLineProgram
 
getNoise() - Method in class picard.illumina.parser.ReadData
 
getNonLogValue(double) - Method in class picard.util.MathUtil.LogMath
Returns the decimal representation of the provided log values.
getNumAdaptersToKeep() - Method in class picard.util.AdapterMarker
 
getNumberOfClusters(File) - Static method in class picard.illumina.parser.readers.BclReader
 
getNumberOfOpticalDuplicateClusters() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getNumClustersInTile() - Method in class picard.illumina.parser.TileIndex.TileIndexRecord
 
getNumDescriptors() - Method in class picard.illumina.parser.ReadStructure
 
getNumDuplicates() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
getNumDuplicates() - Method in class picard.sam.markduplicates.util.MarkQueue
Returns the number of duplicates detected
getNumReads() - Method in class picard.illumina.parser.ClusterData
 
getNumRecordsWithNoMateCigar() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
Useful for statistics after the iterator has been exhausted and closed.
getNumTiles() - Method in class picard.illumina.parser.readers.BclIndexReader
 
getNumTiles() - Method in class picard.illumina.parser.TileIndex
 
getOpticalDupesByLibraryId() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
getOpticalDuplicatesByLibraryIdMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getOrientationByte(boolean, boolean) - Static method in class picard.sam.markduplicates.util.ReadEnds
Returns a single byte that encodes the orientation of the two reads in a pair.
getOutput(RootDoc) - Static method in class picard.util.MetricsDoclet
Gets the file output parameter from the RootDoc and then opens an PrintStream to write to the file.
getOutputCycles() - Method in class picard.illumina.parser.OutputMapping
 
getOutputDescriptors() - Method in class picard.illumina.parser.OutputMapping
 
getOutputFileName(File) - Static method in class picard.sam.CalculateReadGroupChecksum
Creates a file name (not including the path) for an RG MD5 file based on the name of the input file.
getOutputIndexForCycle(int) - Method in class picard.illumina.parser.OutputMapping
Return an index that where: index.arrayIndex - represents either the read number the cycle will be output too, or (in some cases) an array index into a two dimensional array of byte[][] where the top level array corresponds to read number index.elementIndex - represents the element a cycle will appear in inside it's give read, or the element in an array as described above
getOutputReadLengths() - Method in class picard.illumina.parser.OutputMapping
 
getOutputReadStructure() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
Sometimes (in the case of skipped reads) the logical read structure of the output cluster data is different from the input readStructure
getOutputReadStructure() - Method in class picard.illumina.parser.OutputMapping
 
getOutputStream() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
getPackageList() - Static method in class picard.cmdline.PicardCommandLine
The packages we wish to include in our command line
getPaternalId() - Method in class picard.pedigree.PedFile.PedTrio
 
getPerTilePerCycleFiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through all the files for these tiles in expectedBase Side Effect: Assigns numCycles
getPhasingCode(int, IlluminaMetricsCode) - Static method in enum picard.illumina.parser.IlluminaMetricsCode
Phasing codes are between 200 and 299 (inclusive).
getPhasingMap() - Method in class picard.illumina.parser.Tile
 
getPhasingMetricsForTiles(long, Collection<Tile>) - Static method in class picard.illumina.IlluminaPhasingMetrics
Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them
getPhasingValue() - Method in class picard.illumina.parser.TilePhasingValue
 
getPhenotype() - Method in class picard.pedigree.PedFile.PedTrio
 
getPoorQualityFrequencies() - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
Returns a view of number of qualities that failed, where the key is the quality score and the value is the number of observations.
getPrePhasingMap() - Method in class picard.illumina.parser.Tile
 
getPrePhasingValue() - Method in class picard.illumina.parser.TilePhasingValue
 
getProbeIntervals() - Method in class picard.analysis.directed.CalculateHsMetrics
 
getProbeIntervals() - Method in class picard.analysis.directed.CollectTargetedMetrics
 
getProbeIntervals() - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
 
getProbeSetName() - Method in class picard.analysis.directed.CalculateHsMetrics
 
getProbeSetName() - Method in class picard.analysis.directed.CollectTargetedMetrics
 
getProbeSetName() - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
 
getProgramProperty(Class) - Static method in class picard.cmdline.PicardCommandLine
 
getProgramRecord() - Method in class picard.sam.AbstractAlignmentMerger
 
getQualities() - Method in class picard.illumina.parser.BclData
 
getQualities() - Method in class picard.illumina.parser.ReadData
 
getQuerynameSortedAlignedRecords() - Method in class picard.sam.AbstractAlignmentMerger
 
getQuerynameSortedAlignedRecords() - Method in class picard.sam.SamAlignmentMerger
Reads the aligned SAM records into a SortingCollection and returns an iterator over that collection
getRapidDefaultReadNameRegexSplit(String, char, int[]) - Static method in class picard.sam.util.ReadNameParsingUtils
Single pass method to parse the read name for the default regex.
getRawIntensities() - Method in class picard.illumina.parser.ReadData
 
getRead(int) - Method in class picard.illumina.parser.ClusterData
 
getReadEnds() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
Gets the set of read ends
getReadEndSetForOpticalDuplicates() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
Gets the read ends for optical duplicate tracking
getReadGroup() - Method in interface picard.sam.markduplicates.util.OpticalDuplicateFinder.PhysicalLocation
 
getReadGroup() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
getReadGroup() - Method in class picard.sam.markduplicates.util.ReadEnds
 
getReadType() - Method in class picard.illumina.parser.ReadData
 
getRecord() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
getRecordReadName() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
getReferenceSequence() - Method in class picard.metrics.SAMRecordAndReference
 
getSamRecord() - Method in class picard.metrics.SAMRecordAndReference
 
getSamRecordIndex() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
A number of convenience functions
getScatteredFileName(File, long, String) - Static method in class picard.util.IntervalListTools
 
getScheme(boolean) - Method in class picard.vcf.GenotypeConcordanceSchemeFactory
 
getSensitivity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the sensitivity defined by the scheme across the subset of truth states.
getSequenceDictionary() - Method in class picard.sam.AbstractAlignmentMerger
 
getSequentialFileList(File) - Static method in class picard.sam.FastqToSam
Get a list of FASTQs that are sequentially numbered based on the first (base) fastq.
getSex() - Method in class picard.pedigree.PedFile.PedTrio
 
getSnpCounter() - Method in class picard.vcf.GenotypeConcordance
 
getSolexaQualityCharFromFourQualities(String[], int, FormatUtil) - Static method in class picard.util.IlluminaUtil
Get a Solexa ASCII quality value from an array of strings that are integer qualities in this order: [cycle-1-A, cycle-1-C, cycle-1-G, cycle-1-T, cycle-2-A, ...].
getSpecificity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the specificity defined by the scheme across the subset of truth states.
getStandardUsagePreamble(Class) - Static method in class picard.cmdline.CommandLineParser
A typical command line program will call this to get the beginning of the usage message, and then append a description of the program, like this:

\@Usage public String USAGE = CommandLineParser.getStandardUsagePreamble(getClass()) + "Frobnicates the freebozzle."

getStandardUsagePreamble() - Method in class picard.cmdline.CommandLineProgram
 
getSum(Set<GenotypeConcordanceStates.TruthState>, Set<GenotypeConcordanceStates.CallState>) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
getSum() - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
getT() - Method in class picard.illumina.parser.FourChannelIntensityData
 
getTestcases() - Method in class picard.util.TestNGUtil.SingleTestUnitTest
 
getThresholdForSelectingAdaptersToKeep() - Method in class picard.util.AdapterMarker
 
getTile() - Method in class picard.illumina.parser.ClusterData
 
getTile() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
 
getTile() - Method in interface picard.sam.markduplicates.util.OpticalDuplicateFinder.PhysicalLocation
 
getTile() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
getTile() - Method in class picard.sam.markduplicates.util.ReadEnds
 
getTile() - Method in class picard.sam.util.PhysicalLocation
 
getTiledFiles(File, Pattern) - Method in class picard.illumina.parser.ParameterizedFileUtil
Return all files that match pattern of the given file type in the given base directory
getTileFromReadName(String) - Static method in class picard.util.IlluminaUtil
Parse the tile # from the read name.
getTileNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
 
getTileNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
getTileNumber() - Method in class picard.illumina.parser.Tile
Returns the number/name of this tile.
getTileOfNextCluster() - Method in class picard.illumina.parser.MultiTileParser
 
getTileOfNextCluster() - Method in class picard.illumina.parser.PerTileParser
Return the tile of the NEXT ILLUMINA_DATA object to be returned by the method next.
getTiles() - Method in class picard.illumina.parser.MultiTileBclFileUtil
 
getTiles() - Method in class picard.illumina.parser.MultiTileFileUtil
 
getTiles() - Method in class picard.illumina.parser.ParameterizedFileUtil
Return a list of all tiles available for this file format and run
getTiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
Discover all files of this type in expectedBase that match pattern and construct a list of tiles available based on these files.
getTiles() - Method in class picard.illumina.parser.TileIndex
 
getTileTemplateRead() - Method in class picard.illumina.parser.TilePhasingValue
 
getToMarkQueueMinimumDistance() - Method in class picard.sam.markduplicates.util.MarkQueue
Returns the minimum genomic distance such that we can be assured that all duplicates have been considered.
getTotal() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
 
getTotalCycles() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
getTotalInserts() - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
 
getTotalOutputCycles() - Method in class picard.illumina.parser.OutputMapping
 
getTranscriptCoordinate(int) - Method in class picard.annotation.Gene.Transcript
Given a coordinate on the genome (same chromosome) give the corresponding coordinate in the transcript.
getUnmappedBoth() - Method in class picard.sam.CompareSAMs
 
getUnmappedLeft() - Method in class picard.sam.CompareSAMs
 
getUnmappedRight() - Method in class picard.sam.CompareSAMs
 
getUtil(IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.IlluminaFileUtil
Given a file type, get the Parameterized File Util object associated with it
getVar(int, int) - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
 
getVariantTypeFromOrdinal(int) - Static method in enum picard.util.VariantType
Gets the enum for a given ordinal
getVersion() - Method in class picard.cmdline.CommandLineParser
 
getVersion() - Method in class picard.cmdline.CommandLineProgram
 
getWordCount() - Method in class picard.util.AbstractInputParser
 
getX() - Method in class picard.illumina.parser.ClusterData
 
getX() - Method in interface picard.sam.markduplicates.util.OpticalDuplicateFinder.PhysicalLocation
 
getX() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
getX() - Method in class picard.sam.markduplicates.util.ReadEnds
 
getX() - Method in class picard.sam.util.PhysicalLocation
 
getY() - Method in class picard.illumina.parser.ClusterData
 
getY() - Method in interface picard.sam.markduplicates.util.OpticalDuplicateFinder.PhysicalLocation
 
getY() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
getY() - Method in class picard.sam.markduplicates.util.ReadEnds
 
getY() - Method in class picard.sam.util.PhysicalLocation
 
getZeroBasedTileNumber() - Method in class picard.illumina.parser.TileIndex.TileIndexRecord
 

H

handleItem(String) - Method in class picard.cmdline.ClassFinder
Checks an item to see if it is a class and is annotated with the specified annotation.
hasBothParents() - Method in class picard.pedigree.PedFile.PedTrio
True if this record has paternal and maternal ids, otherwise false.
hasColumn(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
hasColumn(String) - Method in class picard.util.TabbedTextFileWithHeaderParser
 
hasCoverage() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
Returns true if any base in the range has coverage of > 1
hashCode() - Method in class picard.annotation.Gene.Transcript
 
hashCode() - Method in class picard.illumina.parser.FourChannelIntensityData
 
hashCode() - Method in class picard.illumina.parser.Range
 
hashCode() - Method in class picard.illumina.parser.ReadDescriptor
 
hashCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
 
hashCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
hashCode() - Method in class picard.illumina.parser.ReadStructure
 
hashCode() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
hasNext() - Method in class picard.illumina.parser.IlluminaDataProvider
 
hasNext() - Method in class picard.illumina.parser.MultiTileParser
 
hasNext() - Method in class picard.illumina.parser.PerTileParser
 
hasNext() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
Return true if the file has more elements to return, false otherwise
hasNext() - Method in class picard.illumina.parser.readers.BarcodeFileReader
 
hasNext() - Method in class picard.illumina.parser.readers.BclReader
 
hasNext() - Method in class picard.illumina.parser.readers.ClocsFileReader
 
hasNext() - Method in class picard.illumina.parser.readers.FilterFileReader
 
hasNext() - Method in class picard.illumina.parser.readers.LocsFileReader
 
hasNext() - Method in class picard.illumina.parser.readers.PosFileReader
 
hasNext() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
 
hasNext() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
hasNext() - Method in class picard.util.AsyncIterator
 
hasNext() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
hasNext() - Method in class picard.vcf.ByIntervalListVariantContextIterator
 
hasNext() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
 
hasNext() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
 
hasWebDocumentation(Class) - Static method in class picard.cmdline.CommandLineParser
Determines if a class has web documentation based on its package name
header - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
 
HEADER - Variable in class picard.sam.ReplaceSamHeader
 
HEADER_ONLY - Variable in class picard.sam.ViewSam
 
headerLines() - Method in class picard.vcf.filter.AlleleBalanceFilter
 
headerLines() - Method in class picard.vcf.filter.FisherStrandFilter
 
headerLines() - Method in class picard.vcf.filter.QdFilter
 
headerLines() - Method in interface picard.vcf.filter.VariantFilter
Return VCF header lines that define filters that may be applied by the VariantFilter.
HET_HOMVAR_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
(count of hets)/(count of homozygous non-ref) for this sample
HET_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP))
HET_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN))
HET_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The specificity for all heterozygous variants cannot be calculated
Histogram_FILE - Variable in class picard.analysis.CollectInsertSizeMetrics
 
Histogram_WIDTH - Variable in class picard.analysis.CollectInsertSizeMetrics
 
HOMVAR_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP))
HOMVAR_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN))
HOMVAR_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The specificity for all homozygous variants cannot be calculated.
HS_LIBRARY_SIZE - Variable in class picard.analysis.directed.HsMetrics
The estimated number of unique molecules in the selected part of the library.
HS_PENALTY_100X - Variable in class picard.analysis.directed.HsMetrics
The "hybrid selection penalty" incurred to get 80% of target bases to 100X.
HS_PENALTY_10X - Variable in class picard.analysis.directed.HsMetrics
The "hybrid selection penalty" incurred to get 80% of target bases to 10X.
HS_PENALTY_20X - Variable in class picard.analysis.directed.HsMetrics
The "hybrid selection penalty" incurred to get 80% of target bases to 20X.
HS_PENALTY_30X - Variable in class picard.analysis.directed.HsMetrics
The "hybrid selection penalty" incurred to get 80% of target bases to 30X.
HS_PENALTY_40X - Variable in class picard.analysis.directed.HsMetrics
The "hybrid selection penalty" incurred to get 80% of target bases to 40X.
HS_PENALTY_50X - Variable in class picard.analysis.directed.HsMetrics
The "hybrid selection penalty" incurred to get 80% of target bases to 50X.
HsMetricCollector - Class in picard.analysis.directed
Calculates HS metrics for a given SAM or BAM file.
HsMetricCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, IntervalList, IntervalList, String) - Constructor for class picard.analysis.directed.HsMetricCollector
 
HsMetrics - Class in picard.analysis.directed
The set of metrics captured that are specific to a hybrid selection analysis.
HsMetrics() - Constructor for class picard.analysis.directed.HsMetrics
 
htmlPrintOptions(PrintStream, boolean) - Method in class picard.cmdline.CommandLineParser
 
htmlUsage(PrintStream, String, boolean) - Method in class picard.cmdline.CommandLineParser
 

I

IGNORE - Variable in class picard.sam.ValidateSamFile
 
IGNORE_SEQUENCE - Variable in class picard.analysis.CollectRnaSeqMetrics
 
IGNORE_THIS_PROPERTY - Variable in class picard.cmdline.CommandLineParser
This attribute is here just to facilitate printing usage for OPTIONS_FILE
IGNORE_WARNINGS - Variable in class picard.sam.ValidateSamFile
 
ignoreAlignment(SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
 
ignoreAlignment(SAMRecord) - Method in class picard.sam.SamAlignmentMerger
For now, we only ignore those alignments that have more than maxGaps insertions or deletions.
IGNORED_READS - Variable in class picard.analysis.RnaSeqMetrics
Number of primary alignments that map to a sequence specified on command-line as IGNORED_SEQUENCE.
Illumina - Class in picard.cmdline.programgroups
 
Illumina() - Constructor for class picard.cmdline.programgroups.Illumina
 
ILLUMINA_ALLEGED_MINIMUM_QUALITY - Static variable in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
 
IlluminaBasecallingMetrics - Class in picard.illumina
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.
IlluminaBasecallingMetrics() - Constructor for class picard.illumina.IlluminaBasecallingMetrics
 
IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
Manages the conversion of Illumina basecalls into some output format.
IlluminaBasecallsConverter(File, int, ReadStructure, Map<String, ? extends IlluminaBasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>>, boolean, int, List<File>, int, boolean, Integer, Integer, Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, BclQualityEvaluationStrategy, boolean, boolean) - Constructor for class picard.illumina.IlluminaBasecallsConverter
 
IlluminaBasecallsConverter(File, File, int, ReadStructure, Map<String, ? extends IlluminaBasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>>, boolean, int, List<File>, int, boolean, Integer, Integer, Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, BclQualityEvaluationStrategy, boolean, boolean) - Constructor for class picard.illumina.IlluminaBasecallsConverter
 
IlluminaBasecallsConverter.ClusterDataConverter<OUTPUT_RECORD> - Interface in picard.illumina
 
IlluminaBasecallsConverter.ConvertedClusterDataWriter<OUTPUT_RECORD> - Interface in picard.illumina
 
IlluminaBasecallsToFastq - Class in picard.illumina
 
IlluminaBasecallsToFastq() - Constructor for class picard.illumina.IlluminaBasecallsToFastq
 
IlluminaBasecallsToFastq.ReadNameFormat - Enum in picard.illumina
Simple switch to control the read name format to emit.
IlluminaBasecallsToSam - Class in picard.illumina
IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into SAM or BAM file format.
IlluminaBasecallsToSam() - Constructor for class picard.illumina.IlluminaBasecallsToSam
 
IlluminaDataProvider - Class in picard.illumina.parser
Parse various formats and versions of Illumina Basecall files, and use them the to populate ClusterData objects.
IlluminaDataProviderFactory - Class in picard.illumina.parser
IlluminaDataProviderFactory accepts options for parsing Illumina data files for a lane and creates an IlluminaDataProvider, an iterator over the ClusterData for that lane, which utilizes these options.
IlluminaDataProviderFactory(File, int, ReadStructure, BclQualityEvaluationStrategy, IlluminaDataType...) - Constructor for class picard.illumina.parser.IlluminaDataProviderFactory
Create factory with the specified options, one that favors using QSeqs over all other files
IlluminaDataProviderFactory(File, File, int, ReadStructure, BclQualityEvaluationStrategy, IlluminaDataType...) - Constructor for class picard.illumina.parser.IlluminaDataProviderFactory
Create factory with the specified options, one that favors using QSeqs over all other files
IlluminaDataType - Enum in picard.illumina.parser
List of data types of interest when parsing Illumina data.
IlluminaFileUtil - Class in picard.illumina.parser
General utils for dealing with IlluminaFiles as well as utils for specific, support formats.
IlluminaFileUtil(File, int) - Constructor for class picard.illumina.parser.IlluminaFileUtil
 
IlluminaFileUtil(File, File, int) - Constructor for class picard.illumina.parser.IlluminaFileUtil
 
IlluminaFileUtil.SupportedIlluminaFormat - Enum in picard.illumina.parser
 
IlluminaLaneMetrics - Class in picard.illumina
Embodies characteristics that describe a lane.
IlluminaLaneMetrics() - Constructor for class picard.illumina.IlluminaLaneMetrics
 
IlluminaMetricsCode - Enum in picard.illumina.parser
Illumina's TileMetricsOut.bin file codes various metrics, both concrete (all density id's are code 100) or as a base code (e.g.
IlluminaPhasingMetrics - Class in picard.illumina
Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
IlluminaPhasingMetrics() - Constructor for class picard.illumina.IlluminaPhasingMetrics
 
IlluminaReadNameEncoder - Class in picard.fastq
A read name encoder following the encoding initially produced by picard fastq writers.
IlluminaReadNameEncoder(String) - Constructor for class picard.fastq.IlluminaReadNameEncoder
 
IlluminaUtil - Class in picard.util
Misc utilities for working with Illumina specific files and data
IlluminaUtil() - Constructor for class picard.util.IlluminaUtil
 
IlluminaUtil.IlluminaAdapterPair - Enum in picard.util
Describes adapters used on each pair of strands
INCLUDE_BQ_HISTOGRAM - Variable in class picard.analysis.CollectWgsMetrics
 
INCLUDE_FILTERED - Variable in class picard.util.IntervalListTools
 
INCLUDE_NO_CALLS - Variable in class picard.analysis.QualityScoreDistribution
 
INCLUDE_NON_PF_READS - Variable in class picard.fastq.BamToBfq
 
INCLUDE_NON_PF_READS - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
INCLUDE_NON_PF_READS - Variable in class picard.illumina.IlluminaBasecallsToSam
 
INCLUDE_NON_PF_READS - Variable in class picard.sam.SamToFastq
 
INCLUDE_NON_PRIMARY_ALIGNMENTS - Variable in class picard.sam.SamToFastq
 
INCLUDE_SECONDARY_ALIGNMENTS - Variable in class picard.sam.MergeBamAlignment
 
INCLUDE_UNPAIRED - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
INCORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
Number of aligned reads that map to the incorrect strand.
increment(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceCounts
Increments a count for the truth/call state tuple.
increment(GenotypeConcordanceStates.TruthAndCallStates, double) - Method in class picard.vcf.GenotypeConcordanceCounts
 
INDEL_OUTPUT - Variable in class picard.vcf.SplitVcfs
 
indelCounter - Variable in class picard.vcf.GenotypeConcordance
 
indels - Variable in class picard.util.DbSnpBitSetUtil.DbSnpBitSets
 
indexOfMax(double[]) - Static method in class picard.util.MathUtil
Returns the index of the largest element in the array.
inferArtifactName() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
Label the artifacts corresponding to known error modes.
inferArtifactName() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
Label the artifacts corresponding to known error modes.
initialize() - Method in class picard.illumina.parser.MultiTileBclParser
 
initiateScheme() - Method in class picard.vcf.GA4GHScheme
 
initiateScheme() - Method in class picard.vcf.GA4GHSchemeWithMissingAsHomRef
 
initiateScheme() - Method in class picard.vcf.GenotypeConcordanceScheme
 
INPUT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
 
INPUT - Variable in class picard.analysis.CollectMultipleMetrics
 
INPUT - Variable in class picard.analysis.CollectOxoGMetrics
 
INPUT - Variable in class picard.analysis.CollectQualityYieldMetrics
 
INPUT - Variable in class picard.analysis.CollectRrbsMetrics
 
INPUT - Variable in class picard.analysis.CollectWgsMetrics
 
INPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
INPUT - Variable in class picard.analysis.SinglePassSamProgram
 
INPUT - Variable in class picard.fastq.BamToBfq
 
INPUT - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
 
INPUT - Variable in class picard.illumina.MarkIlluminaAdapters
 
INPUT - Variable in class picard.reference.NormalizeFasta
 
INPUT - Variable in class picard.sam.AddCommentsToBam
 
INPUT - Variable in class picard.sam.AddOrReplaceReadGroups
 
INPUT - Variable in class picard.sam.BamIndexStats
 
INPUT - Variable in class picard.sam.BuildBamIndex
 
INPUT - Variable in class picard.sam.CalculateReadGroupChecksum
 
INPUT - Variable in class picard.sam.CheckTerminatorBlock
 
INPUT - Variable in class picard.sam.CleanSam
 
INPUT - Variable in class picard.sam.DownsampleSam
 
INPUT - Variable in class picard.sam.FilterSamReads
 
INPUT - Variable in class picard.sam.FixMateInformation
 
INPUT - Variable in class picard.sam.GatherBamFiles
 
INPUT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
INPUT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
INPUT - Variable in class picard.sam.MergeSamFiles
 
INPUT - Variable in class picard.sam.PositionBasedDownsampleSam
 
INPUT - Variable in class picard.sam.ReorderSam
 
INPUT - Variable in class picard.sam.ReplaceSamHeader
 
INPUT - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
INPUT - Variable in class picard.sam.RevertSam
 
INPUT - Variable in class picard.sam.SamFormatConverter
 
INPUT - Variable in class picard.sam.SamToFastq
 
INPUT - Variable in class picard.sam.SortSam
 
INPUT - Variable in class picard.sam.SplitSamByLibrary
 
INPUT - Variable in class picard.sam.ValidateSamFile
 
INPUT - Variable in class picard.sam.ViewSam
 
INPUT - Variable in class picard.util.BedToIntervalList
 
INPUT - Variable in class picard.util.IntervalListTools
 
INPUT - Variable in class picard.util.LiftOverIntervalList
 
INPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
 
INPUT - Variable in class picard.vcf.filter.FilterVcf
 
INPUT - Variable in class picard.vcf.GatherVcfs
 
INPUT - Variable in class picard.vcf.LiftoverVcf
 
INPUT - Variable in class picard.vcf.MakeSitesOnlyVcf
 
INPUT - Variable in class picard.vcf.MergeVcfs
 
INPUT - Variable in class picard.vcf.RenameSampleInVcf
 
INPUT - Variable in class picard.vcf.SortVcf
 
INPUT - Variable in class picard.vcf.SplitVcfs
 
INPUT - Variable in class picard.vcf.UpdateVcfSequenceDictionary
 
INPUT - Variable in class picard.vcf.VcfFormatConverter
 
INPUT - Variable in class picard.vcf.VcfToIntervalList
 
INPUT_BASE - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 
INPUT_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
InsertSizeMetrics - Class in picard.analysis
Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension ".insert_size_metrics".
InsertSizeMetrics() - Constructor for class picard.analysis.InsertSizeMetrics
 
InsertSizeMetricsCollector - Class in picard.analysis.directed
Collects InserSizeMetrics on the specified accumulationLevels using
InsertSizeMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, double, Integer, double) - Constructor for class picard.analysis.directed.InsertSizeMetricsCollector
 
InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector - Class in picard.analysis.directed
A Collector for individual InsertSizeMetrics for a given SAMPLE or SAMPLE/LIBRARY or SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels)
InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector(String, String, String) - Constructor for class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
 
instanceMain(String[]) - Method in class picard.cmdline.CommandLineProgram
 
instanceMain(String[], List<String>, String) - Method in class picard.cmdline.PicardCommandLine
The main method.
instanceMain(String[]) - Method in class picard.cmdline.PicardCommandLine
For testing
instanceMainWithExit(String[]) - Method in class picard.cmdline.CommandLineProgram
 
IntensityChannel - Enum in picard.illumina.parser
The channels in a FourChannelIntensityData object, and the channels produced by a ClusterIntensityFileReader, for cases in which it is desirable to handle these abstractly rather than having the specific names in the source code.
INTERGENIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
Number of bases in primary aligments that do not align to any gene.
INTERLEAVE - Variable in class picard.sam.SamToFastq
 
INTEROP_SUBDIRECTORY_NAME - Static variable in class picard.illumina.parser.TileMetricsUtil
The path to the directory containing the tile metrics file relative to the basecalling directory.
INTERSECT_INTERVALS - Variable in class picard.vcf.GenotypeConcordance
 
INTERVAL_LIST - Variable in class picard.reference.ExtractSequences
 
INTERVAL_LIST - Variable in class picard.sam.ViewSam
 
IntervalListScatterer - Class in picard.util
 
IntervalListScatterer(IntervalListScatterer.Mode) - Constructor for class picard.util.IntervalListScatterer
 
IntervalListScatterer.Mode - Enum in picard.util
 
IntervalListTools - Class in picard.util
Little class to aid working with interval lists.
IntervalListTools() - Constructor for class picard.util.IntervalListTools
 
IntervalListTools.Action - Enum in picard.util
 
INTERVALS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
INTERVALS - Variable in class picard.analysis.CollectOxoGMetrics
 
Intervals - Class in picard.cmdline.programgroups
 
Intervals() - Constructor for class picard.cmdline.programgroups.Intervals
 
INTERVALS - Variable in class picard.vcf.GenotypeConcordance
 
INTRONIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
Number of bases in primary aligments that align to an intronic base for some gene, and not a coding or UTR base.
INVERT - Variable in class picard.util.IntervalListTools
 
IO_SIZE - Variable in class picard.util.FifoBuffer
 
IS_BISULFITE_SEQUENCE - Variable in class picard.sam.MergeBamAlignment
 
IS_BISULFITE_SEQUENCED - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
 
IS_BISULFITE_SEQUENCED - Variable in class picard.analysis.CollectGcBiasMetrics
 
IS_BISULFITE_SEQUENCED - Variable in class picard.sam.ValidateSamFile
 
isBlank(byte[]) - Method in class picard.util.AbstractInputParser
Determines whether a given line is a comment
isBlockGzipped(File) - Static method in class picard.illumina.parser.readers.BclReader
 
isClipOverlappingReads() - Method in class picard.sam.AbstractAlignmentMerger
 
isClosed() - Method in class picard.util.CircularByteBuffer
Returns true if the buffer is closed, false otherwise.
isComment(byte[]) - Method in class picard.util.AbstractInputParser
Determines whether a given line is a comment
isDbSnpSite(String, int) - Method in class picard.util.DbSnpBitSetUtil
Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false
isDelimiter(byte) - Method in class picard.util.AbstractInputParser
Determines whether a given character is a delimiter
isDelimiter(byte) - Method in class picard.util.CsvInputParser
Determines whether a given character is a delimiter
isDelimiter(byte) - Method in class picard.util.TabbedInputParser
Determines whether a given character is a delimiter
isEmpty() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
isEmpty() - Method in class picard.sam.markduplicates.util.MarkQueue
 
isGzipped(File) - Static method in class picard.illumina.parser.readers.BclReader
 
isKeepAlignerProperPairFlags() - Method in class picard.sam.AbstractAlignmentMerger
 
isMetricsClass(ClassDoc) - Static method in class picard.util.MetricsDoclet
Checks to see if the class extends MetricBase using only the JavaDoc metadata provided about the class.
isMissing(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns true if EITHER the truth or call state is MISSING.
isPaired() - Method in class picard.sam.markduplicates.util.ReadEnds
 
isPaired() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
isPf() - Method in class picard.illumina.parser.ClusterData
 
isPhasing(IlluminaMetricsCode) - Static method in enum picard.illumina.parser.IlluminaMetricsCode
 
isReservedTag(String) - Method in class picard.sam.AbstractAlignmentMerger
 
isSkipBlankLines() - Method in class picard.util.AbstractInputParser
 
isSoloTranscript() - Method in class picard.annotation.Gene.Transcript
 
isTreatGroupedDelimitersAsOne() - Method in class picard.util.AbstractInputParser
 
isVar(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns true if EITHER the truth or call state is a VAR.
iterator() - Method in class picard.annotation.Gene
 
iterator() - Method in class picard.illumina.parser.IlluminaDataProvider
 
iterator() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
iterator() - Method in class picard.illumina.parser.TileIndex
 
iterator - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
 
iterator() - Method in class picard.util.AbstractInputParser
 
iterator() - Method in class picard.util.TabbedTextFileWithHeaderParser
Creates the iterator object.
Iterators - Class in picard.util
 
Iterators() - Constructor for class picard.util.Iterators
 
iterators() - Method in class picard.vcf.processor.VariantIteratorProducer
Renders the embodied regions of the VCF files in the form of CloseableIterators over VariantContexts.

J

JUMP_DUPLICATE_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of outward-facing pairs that are duplicates
JUMP_DUPLICATE_PCT - Variable in class picard.analysis.JumpingLibraryMetrics
The percentage of outward-facing pairs that are marked as duplicates
JUMP_LIBRARY_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
The estimated library size for outward-facing pairs
JUMP_MEAN_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
The mean insert size for outward-facing pairs
JUMP_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of outward-facing pairs in the SAM file
JUMP_SIZE - Variable in class picard.sam.MergeBamAlignment
 
JUMP_STDEV_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
The standard deviation on the insert size for outward-facing pairs
JumpingLibraryMetrics - Class in picard.analysis
High level metrics about the presence of outward- and inward-facing pairs within a SAM file generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".
JumpingLibraryMetrics() - Constructor for class picard.analysis.JumpingLibraryMetrics
 

L

LANE - Variable in class picard.fastq.BamToBfq
 
LANE - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
 
LANE - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
LANE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The lane for which the metrics were calculated.
LANE - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
LANE - Variable in class picard.illumina.IlluminaBasecallsToSam
 
LANE - Variable in class picard.illumina.IlluminaLaneMetrics
This lane's number.
LANE - Variable in class picard.illumina.IlluminaPhasingMetrics
 
lane - Variable in class picard.illumina.parser.ParameterizedFileUtil
 
lane - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
The lane, which is determined from the file name
LANE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
LANE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
laneIsSet() - Method in class picard.illumina.parser.ClusterData
 
LanePhasingMetricsCollector - Class in picard.illumina
Helper class used to transform tile data for a lane into a collection of IlluminaPhasingMetrics
LanePhasingMetricsCollector(Collection<Tile>) - Constructor for class picard.illumina.LanePhasingMetricsCollector
Constructor takes a lane's collection of Tiles and calculates the median phasing/prephasing for the first and second (if available) reads
LANES - Variable in class picard.illumina.CheckIlluminaDirectory
 
LEFT_PRIMER - Variable in class picard.util.BaitDesigner
 
length() - Method in class picard.annotation.Gene.Transcript
 
length - Variable in class picard.illumina.parser.Range
 
length - Variable in class picard.illumina.parser.ReadDescriptor
 
length() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The name of the library being assayed.
LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The name of the library being assayed.
LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The name of the library being assayed.
LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The name of the library being assayed.
LIBRARY - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The name of the library being assayed.
LIBRARY - Variable in class picard.metrics.MultilevelMetrics
The library to which these metrics apply.
LIBRARY - Variable in class picard.sam.DuplicationMetrics
The library on which the duplicate marking was performed.
LIBRARY_NAME - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
 
LIBRARY_NAME - Variable in class picard.illumina.IlluminaBasecallsToSam
 
LIBRARY_NAME - Variable in class picard.sam.FastqToSam
 
LIBRARY_NAME - Variable in class picard.sam.RevertSam
 
LIBRARY_NAME_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
LIBRARY_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToSam
 
libraryId - Variable in class picard.sam.markduplicates.util.ReadEnds
 
libraryIdGenerator - Variable in class picard.sam.markduplicates.MarkDuplicates
 
LibraryIdGenerator - Class in picard.sam.markduplicates.util
A class to generate library Ids and keep duplication metrics by library IDs.
LibraryIdGenerator(SAMFileHeader) - Constructor for class picard.sam.markduplicates.util.LibraryIdGenerator
 
LiftOverIntervalList - Class in picard.util
 
LiftOverIntervalList() - Constructor for class picard.util.LiftOverIntervalList
 
LiftoverVcf - Class in picard.vcf
Tool for lifting over a VCF to another genome build and producing a properly header'd, sorted and indexed VCF in one go.
LiftoverVcf() - Constructor for class picard.vcf.LiftoverVcf
 
limitingProcessedRegionsTo(IntervalList) - Method in class picard.vcf.processor.VariantProcessor.Builder
 
LINE_LENGTH - Variable in class picard.reference.ExtractSequences
 
LINE_LENGTH - Variable in class picard.reference.NormalizeFasta
 
LINK_LOCS - Variable in class picard.illumina.CheckIlluminaDirectory
 
loadRefFlat(File, SAMSequenceDictionary) - Static method in class picard.annotation.GeneAnnotationReader
 
LocsFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
LocsFileFaker() - Constructor for class picard.illumina.parser.fakers.LocsFileFaker
 
LocsFileReader - Class in picard.illumina.parser.readers
The locs file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
LocsFileReader(File) - Constructor for class picard.illumina.parser.readers.LocsFileReader
 
LocsFileReader(File, int, int) - Constructor for class picard.illumina.parser.readers.LocsFileReader
 
LocusFunction - Enum in picard.annotation
Describes the behavior of a locus relative to a gene.
LOG - Static variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
LOG - Static variable in class picard.vcf.VcfFormatConverter
 
LOG - Static variable in class picard.vcf.VcfToIntervalList
 
log10_1p(double) - Static method in class picard.util.MathUtil
this function mimics the behavior of log_1p but resulting in log _base 10_ of (1+x) instead of natural log of 1+x
LOG_10_MATH - Static variable in class picard.util.MathUtil
 
LOG_2_MATH - Static variable in class picard.util.MathUtil
 
logLikelihoodsToProbs(double[]) - Static method in class picard.util.MathUtil
Deprecated.
logMemoryStats(Log) - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
longLaneStr(int) - Static method in class picard.illumina.parser.IlluminaFileUtil
 

M

MACHINE_NAME - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
MAD_COVERAGE - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The median absolute deviation of coverage of the genome after all filters are applied.
main(String[]) - Static method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
main(String[]) - Static method in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 
main(String[]) - Static method in class picard.analysis.CollectAlignmentSummaryMetrics
Required main method implementation.
main(String[]) - Static method in class picard.analysis.CollectBaseDistributionByCycle
 
main(String[]) - Static method in class picard.analysis.CollectGcBiasMetrics
 
main(String[]) - Static method in class picard.analysis.CollectInsertSizeMetrics
Required main method implementation.
main(String[]) - Static method in class picard.analysis.CollectJumpingLibraryMetrics
Stock main method.
main(String[]) - Static method in class picard.analysis.CollectMultipleMetrics
 
main(String[]) - Static method in class picard.analysis.CollectOxoGMetrics
 
main(String[]) - Static method in class picard.analysis.CollectQualityYieldMetrics
Stock main method for a command line program.
main(String[]) - Static method in class picard.analysis.CollectRnaSeqMetrics
Required main method implementation.
main(String[]) - Static method in class picard.analysis.CollectRrbsMetrics
 
main(String[]) - Static method in class picard.analysis.CollectWgsMetrics
 
main(String[]) - Static method in class picard.analysis.CompareMetrics
 
main(String[]) - Static method in class picard.analysis.directed.CalculateHsMetrics
Stock main method.
main(String[]) - Static method in class picard.analysis.directed.CollectTargetedPcrMetrics
Stock main method.
main(String[]) - Static method in class picard.analysis.MeanQualityByCycle
Required main method.
main(String[]) - Static method in class picard.analysis.QualityScoreDistribution
Required main method.
main(String[]) - Static method in class picard.cmdline.CreateHtmlDocForProgram
 
main(String[]) - Static method in class picard.cmdline.CreateHtmlDocForStandardOptions
 
main(String[]) - Static method in class picard.cmdline.PicardCommandLine
Override this if you want to include different java packages to search for classes that extend CommandLineProgram.
main(String[]) - Static method in class picard.fastq.BamToBfq
 
main(String[]) - Static method in class picard.illumina.CheckIlluminaDirectory
Required main method implementation.
main(String[]) - Static method in class picard.illumina.CollectIlluminaBasecallingMetrics
 
main(String[]) - Static method in class picard.illumina.CollectIlluminaLaneMetrics
 
main(String[]) - Static method in class picard.illumina.ExtractIlluminaBarcodes
 
main(String[]) - Static method in class picard.illumina.IlluminaBasecallsToFastq
 
main(String[]) - Static method in class picard.illumina.IlluminaBasecallsToSam
 
main(String[]) - Static method in class picard.illumina.MarkIlluminaAdapters
 
main(String[]) - Static method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
Stock main method.
main(String[]) - Static method in class picard.reference.ExtractSequences
 
main(String[]) - Static method in class picard.reference.NormalizeFasta
 
main(String[]) - Static method in class picard.sam.AddCommentsToBam
 
main(String[]) - Static method in class picard.sam.AddOrReplaceReadGroups
Required main method implementation.
main(String[]) - Static method in class picard.sam.BamIndexStats
Stock main method for a command line program.
main(String[]) - Static method in class picard.sam.BuildBamIndex
Stock main method for a command line program.
main(String[]) - Static method in class picard.sam.CalculateReadGroupChecksum
 
main(String[]) - Static method in class picard.sam.CheckTerminatorBlock
 
main(String[]) - Static method in class picard.sam.CleanSam
 
main(String[]) - Static method in class picard.sam.CompareSAMs
 
main(String[]) - Static method in class picard.sam.CreateSequenceDictionary
 
main(String[]) - Static method in class picard.sam.DownsampleSam
 
main(String[]) - Static method in class picard.sam.DuplicationMetrics
 
main(String[]) - Static method in class picard.sam.FastqToSam
Stock main method.
main(String[]) - Static method in class picard.sam.FilterSamReads
Stock main method.
main(String[]) - Static method in class picard.sam.FixMateInformation
 
main(String[]) - Static method in class picard.sam.GatherBamFiles
 
main(String[]) - Static method in class picard.sam.markduplicates.EstimateLibraryComplexity
Stock main method.
main(String[]) - Static method in class picard.sam.markduplicates.MarkDuplicates
Stock main method.
main(String[]) - Static method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
Stock main method.
main(String[]) - Static method in class picard.sam.MergeBamAlignment
Required main method implementation.
main(String[]) - Static method in class picard.sam.MergeSamFiles
Required main method implementation.
main(String[]) - Static method in class picard.sam.PositionBasedDownsampleSam
 
main(String[]) - Static method in class picard.sam.ReorderSam
Required main method implementation.
main(String[]) - Static method in class picard.sam.ReplaceSamHeader
 
main(String[]) - Static method in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
Default main method impl.
main(String[]) - Static method in class picard.sam.RevertSam
Default main method impl.
main(String[]) - Static method in class picard.sam.SamFormatConverter
 
main(String[]) - Static method in class picard.sam.SamToFastq
 
main(String[]) - Static method in class picard.sam.SortSam
 
main(String[]) - Static method in class picard.sam.SplitSamByLibrary
 
main(String[]) - Static method in class picard.sam.ValidateSamFile
 
main(String[]) - Static method in class picard.sam.ViewSam
 
main(String[]) - Static method in class picard.Test
 
main(String[]) - Static method in class picard.util.BaitDesigner
Stock main method.
main(String[]) - Static method in class picard.util.BedToIntervalList
 
main(String[]) - Static method in class picard.util.FifoBuffer
 
main(String[]) - Static method in class picard.util.IntervalListTools
 
main(String[]) - Static method in class picard.util.LiftOverIntervalList
 
main(String[]) - Static method in class picard.util.ScatterIntervalsByNs
 
main(String[]) - Static method in class picard.vcf.CollectVariantCallingMetrics
 
main(String[]) - Static method in class picard.vcf.filter.FilterVcf
 
main(String[]) - Static method in class picard.vcf.GatherVcfs
 
main(String[]) - Static method in class picard.vcf.GenotypeConcordance
 
main(String[]) - Static method in class picard.vcf.LiftoverVcf
 
main(String[]) - Static method in class picard.vcf.MakeSitesOnlyVcf
 
main(String[]) - Static method in class picard.vcf.MergeVcfs
 
main(String[]) - Static method in class picard.vcf.RenameSampleInVcf
 
main(String[]) - Static method in class picard.vcf.SortVcf
 
main(String[]) - Static method in class picard.vcf.SplitVcfs
 
main(String[]) - Static method in class picard.vcf.UpdateVcfSequenceDictionary
 
main(String[]) - Static method in class picard.vcf.VcfFormatConverter
 
main(String[]) - Static method in class picard.vcf.VcfToIntervalList
 
makeAllReadCollector() - Method in class picard.analysis.directed.TargetMetricsCollector
 
makeAllReadCollector() - Method in class picard.metrics.MultiLevelCollector
 
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.GcBiasMetricsCollector
 
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
 
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.MultiLevelCollector
 
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
 
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.SAMRecordMultiLevelCollector
 
makeChildCollector(String, String, String) - Method in class picard.analysis.AlignmentSummaryMetricsCollector
 
makeChildCollector(String, String, String) - Method in class picard.analysis.directed.GcBiasMetricsCollector
 
makeChildCollector(String, String, String) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
Make an InsertSizeCollector with the given arguments
makeChildCollector(String, String, String) - Method in class picard.analysis.directed.RnaSeqMetricsCollector
 
makeChildCollector(String, String, String) - Method in class picard.analysis.directed.TargetMetricsCollector
 
makeChildCollector(String, String, String) - Method in class picard.analysis.RrbsMetricsCollector
 
makeChildCollector(String, String, String) - Method in class picard.metrics.MultiLevelCollector
Construct a PerUnitMetricCollector with the given arguments.
makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, IntervalList, IntervalList, String) - Method in class picard.analysis.directed.CalculateHsMetrics
 
makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, IntervalList, IntervalList, String) - Method in class picard.analysis.directed.CollectTargetedMetrics
A factory method for the TargetMetricsCollector to use this time.
makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, IntervalList, IntervalList, String) - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
 
makeCycleFileParser(List<File>) - Method in class picard.illumina.parser.MultiTileBclParser
 
makeDataProvider() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
Call this method to create a ClusterData iterator over all clusters for all tiles in ascending numeric order.
makeDataProvider(List<Integer>) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
Call this method to create a ClusterData iterator over the specified tiles.
makeExceptionMsg() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
Create a string that will be included in any NoSuchElementException thrown by the next() method
makeExceptionMsg() - Method in class picard.illumina.parser.readers.ClocsFileReader
 
makeExceptionMsg() - Method in class picard.illumina.parser.readers.LocsFileReader
 
makeExceptionMsg() - Method in class picard.illumina.parser.readers.PosFileReader
 
makeIgnoredSequenceIndicesSet(SAMFileHeader, Set<String>) - Static method in class picard.analysis.directed.RnaSeqMetricsCollector
 
makeInstance(String, File, File) - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
 
makeItSo(File, File, boolean, long, Collection<SinglePassSamProgram>) - Static method in class picard.analysis.SinglePassSamProgram
 
makeItSo(FastqReader, FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
Handles the FastqToSam execution on the FastqReader(s).
makeLaneTileRegex(String, int) - Static method in class picard.illumina.parser.ParameterizedFileUtil
Return a regex string for finding Lane and Tile given a file extension pattern
makeLibraryCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
 
makeOverlapDetector(File, SAMFileHeader, File) - Static method in class picard.analysis.directed.RnaSeqMetricsCollector
 
makePhredBinaryFromSolexaQualityAscii_1_3(String) - Static method in class picard.util.IlluminaUtil
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
makePhredBinaryFromSolexaQualityAscii_1_3(String, int, int) - Static method in class picard.util.IlluminaUtil
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
makeReadGroupCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
 
makeSampleCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
 
makeSeekable(List<File>, BclQualityEvaluationStrategy, int[]) - Static method in class picard.illumina.parser.readers.BclReader
 
makeSequenceDictionary(File) - Method in class picard.sam.CreateSequenceDictionary
Read all the sequences from the given reference file, and convert into SAMSequenceRecords
MakeSitesOnlyVcf - Class in picard.vcf
Writes out a VCF that contains all the site-level information for all records in the input VCF and no per-sample information.
MakeSitesOnlyVcf() - Constructor for class picard.vcf.MakeSitesOnlyVcf
 
makeTileIterator(File) - Method in class picard.illumina.parser.PerTileParser
Factory method for the iterator of each tile
makeTileIterator(File) - Method in class picard.illumina.parser.PosParser
Make an CloseableIterator based on the given file and fileType specified at construction.
MarkDuplicates - Class in picard.sam.markduplicates
A better duplication marking algorithm that handles all cases including clipped and gapped alignments.
MarkDuplicates() - Constructor for class picard.sam.markduplicates.MarkDuplicates
 
MarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
An even better duplication marking algorithm that handles all cases including clipped and gapped alignments.
MarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
 
MarkDuplicatesWithMateCigarIterator - Class in picard.sam.markduplicates
This will iterate through a coordinate sorted SAM file (iterator) and either mark or remove duplicates as appropriate.
MarkDuplicatesWithMateCigarIterator(SAMFileHeader, CloseableIterator<SAMRecord>, OpticalDuplicateFinder, DuplicateScoringStrategy.ScoringStrategy, int, boolean, boolean, int, int, List<File>) - Constructor for class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
Initializes the mark duplicates iterator.
MarkIlluminaAdapters - Class in picard.illumina
Command line program to mark the location of adapter sequences.
MarkIlluminaAdapters() - Constructor for class picard.illumina.MarkIlluminaAdapters
 
MarkQueue - Class in picard.sam.markduplicates.util
This is the mark queue.
MarkQueue(DuplicateScoringStrategy.ScoringStrategy) - Constructor for class picard.sam.markduplicates.util.MarkQueue
 
matchPattern - Variable in class picard.illumina.parser.ParameterizedFileUtil
A pattern that will match files of this type for this lane
MathUtil - Class in picard.util
General math utilities
MathUtil.LogMath - Class in picard.util
A collection of common math operations that work with log values.
max(double[]) - Static method in class picard.util.MathUtil
Returns the largest value stored in the array.
MAX_DIFF_RATE - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
MAX_DISCARD_FRACTION - Variable in class picard.sam.RevertSam
 
MAX_ERROR_RATE - Static variable in class picard.util.ClippingUtility
The default value used for the maximum error rate when matching read bases to clippable sequence.
MAX_ERROR_RATE_PE - Variable in class picard.illumina.MarkIlluminaAdapters
 
MAX_ERROR_RATE_SE - Variable in class picard.illumina.MarkIlluminaAdapters
 
MAX_FILE_HANDLES_FOR_READ_ENDS_MAP - Variable in class picard.sam.markduplicates.MarkDuplicates
 
MAX_FS - Variable in class picard.vcf.filter.FilterVcf
 
MAX_GROUP_RATIO - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
MAX_INSERT_SIZE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
 
MAX_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
The maximum measure insert size by alignment.
MAX_INSERTIONS_OR_DELETIONS - Variable in class picard.sam.MergeBamAlignment
 
MAX_MISMATCH_RATE - Variable in class picard.analysis.CollectRrbsMetrics
 
MAX_MISMATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
MAX_NO_CALLS - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
MAX_OPEN_TEMP_FILES - Variable in class picard.sam.ValidateSamFile
 
MAX_OUTPUT - Variable in class picard.sam.ValidateSamFile
 
MAX_PE_ERROR_RATE - Static variable in class picard.util.ClippingUtility
The default value used for the maximum error rate when matching paired end read bases to clippable sequence.
MAX_POS - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
 
MAX_PROB_BELOW_ONE - Static variable in class picard.util.MathUtil
The double value closest to 1 while still being less than 1.
MAX_Q - Variable in class picard.sam.FastqToSam
 
MAX_READS_IN_RAM_PER_TILE - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
MAX_READS_IN_RAM_PER_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
 
MAX_RECORDS_IN_RAM - Variable in class picard.cmdline.CommandLineProgram
 
MAX_RECORDS_IN_RAM - Static variable in class picard.sam.AbstractAlignmentMerger
 
MAX_RECORDS_TO_EXAMINE - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP - Variable in class picard.sam.markduplicates.MarkDuplicates
If more than this many sequences in SAM file, don't spill to disk because there will not be enough file handles.
MAX_TO_MERGE - Variable in class picard.util.ScatterIntervalsByNs
 
MAXIMUM_INSERT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
MAXIMUM_INSERT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
 
maybeAdvance() - Method in class picard.illumina.parser.PerTileParser
 
mean(double...) - Method in class picard.util.MathUtil.LogMath
Computes the mean of the provided log values.
mean(double[], int, int) - Static method in class picard.util.MathUtil
Calculated the mean of an array of doubles.
MEAN_AMPLICON_COVERAGE - Variable in class picard.analysis.directed.TargetedPcrMetrics
The mean coverage of all amplicons in the experiment.
MEAN_BAIT_COVERAGE - Variable in class picard.analysis.directed.HsMetrics
The mean coverage of all baits in the experiment.
MEAN_BASE_QUALITY - Variable in class picard.analysis.GcBiasDetailMetrics
The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.
MEAN_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The mean number of clusters per tile.
MEAN_COVERAGE - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The mean coverage in bases of the genome territory, after all filters are applied.
MEAN_CPG_COVERAGE - Variable in class picard.analysis.RrbsSummaryMetrics
Mean coverage of CpG sites
MEAN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
The mean insert size of the "core" of the distribution.
MEAN_PCT_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The mean percentage of pf clusters per tile.
MEAN_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The mean number of pf clusters per tile.
MEAN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
The mean read length of the set of reads examined.
MEAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.HsMetrics
The mean coverage of targets that received at least coverage depth = 2 at one base.
MEAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.TargetedPcrMetrics
The mean coverage of targets that recieved at least coverage depth = 2 at one base.
MeanQualityByCycle - Class in picard.analysis
Program to generate a data table and chart of mean quality by cycle from a BAM file.
MeanQualityByCycle() - Constructor for class picard.analysis.MeanQualityByCycle
 
median(double...) - Static method in class picard.util.MathUtil
Calculate the median of an array of doubles.
MEDIAN_3PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
The median 3 prime bias of the 1000 most highly expressed transcripts, where 3 prime bias is calculated per transcript as: mean coverage of the 3' most 100 bases divided by the mean coverage of the whole transcript.
MEDIAN_5PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
The median 5 prime bias of the 1000 most highly expressed transcripts, where 5 prime bias is calculated per transcript as: mean coverage of the 5' most 100 bases divided by the mean coverage of the whole transcript.
MEDIAN_5PRIME_TO_3PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
The ratio of coverage at the 5' end of to the 3' end based on the 1000 most highly expressed transcripts.
MEDIAN_ABSOLUTE_DEVIATION - Variable in class picard.analysis.InsertSizeMetrics
The median absolute deviation of the distribution.
MEDIAN_COVERAGE - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The median coverage in bases of the genome territory, after all filters are applied.
MEDIAN_CPG_COVERAGE - Variable in class picard.analysis.RrbsSummaryMetrics
Median coverage of CpG sites
MEDIAN_CV_COVERAGE - Variable in class picard.analysis.RnaSeqMetrics
The median CV of coverage of the 1000 most highly expressed transcripts.
MEDIAN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.
merge(ExtractIlluminaBarcodes.BarcodeMetric) - Method in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
Adds the non-calculated
merge(CollectHiSeqXPfFailMetrics.PFFailSummaryMetric) - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
Adds the non-calculated fields from the other metric to this one.
merge(Collection<CallingMetricAccumulator.Result>) - Static method in class picard.vcf.CallingMetricAccumulator.Result
 
merge(Collection<RESULT>) - Method in interface picard.vcf.processor.VariantProcessor.ResultMerger
 
MERGE_NEARBY_TARGETS - Variable in class picard.util.BaitDesigner
 
MERGE_SEQUENCE_DICTIONARIES - Variable in class picard.sam.MergeSamFiles
 
mergeAlignment(File) - Method in class picard.sam.AbstractAlignmentMerger
/** Merges the alignment data with the non-aligned records from the source BAM file.
mergeAlignment(File) - Method in class picard.sam.SamAlignmentMerger
Merges the alignment from the map file with the non-aligned records from the source BAM file.
MergeBamAlignment - Class in picard.sam
A command-line tool to merge BAM/SAM alignment info from a third-party aligner with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM
MergeBamAlignment() - Constructor for class picard.sam.MergeBamAlignment
 
MergeSamFiles - Class in picard.sam
Reads a SAM or BAM file and combines the output to one file
MergeSamFiles() - Constructor for class picard.sam.MergeSamFiles
 
MergeVcfs - Class in picard.vcf
Combines multiple VCF files into a single file.
MergeVcfs() - Constructor for class picard.vcf.MergeVcfs
 
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectGcBiasMetrics
 
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectRrbsMetrics
 
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
MetricAccumulationLevel - Enum in picard.analysis
For use with Picard metrics programs that may output metrics for multiple levels of aggregation with an analysis.
Metrics - Class in picard.cmdline.programgroups
 
Metrics() - Constructor for class picard.cmdline.programgroups.Metrics
 
METRICS - Variable in class picard.illumina.MarkIlluminaAdapters
 
METRICS_FILE - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
METRICS_FILE - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
METRICS_FILE_PREFIX - Variable in class picard.analysis.CollectRrbsMetrics
 
METRICS_FILE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
MetricsDoclet - Class in picard.util
Doclet for use with JavaDoc that will find all classes extending MetricBase and output information about the metrics definitions that go along with the classes.
MetricsDoclet() - Constructor for class picard.util.MetricsDoclet
 
metricsFiles - Variable in class picard.analysis.CompareMetrics
 
min(double[]) - Static method in class picard.util.MathUtil
Returns the smallest value stored in the array.
min(short[]) - Static method in class picard.util.MathUtil
Returns the smallest value stored in the array.
MIN_AB - Variable in class picard.vcf.filter.FilterVcf
 
MIN_DP - Variable in class picard.vcf.filter.FilterVcf
 
MIN_DP - Variable in class picard.vcf.GenotypeConcordance
 
MIN_GQ - Variable in class picard.vcf.filter.FilterVcf
 
MIN_GQ - Variable in class picard.vcf.GenotypeConcordance
 
MIN_IDENTICAL_BASES - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
MIN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
The minimum measured insert size.
MIN_LIFTOVER_PCT - Variable in class picard.util.LiftOverIntervalList
 
MIN_MATCH_BASES - Static variable in class picard.util.ClippingUtility
The default value used for the minimum number of contiguous bases to match against.
MIN_MATCH_BASES_PE - Variable in class picard.illumina.MarkIlluminaAdapters
 
MIN_MATCH_BASES_SE - Variable in class picard.illumina.MarkIlluminaAdapters
 
MIN_MATCH_PE_BASES - Static variable in class picard.util.ClippingUtility
The default value used for the minimum number of contiguous bases to match against in a paired end read
MIN_MEAN_QUALITY - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
MIN_MISMATCH_DELTA - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
MIN_POS - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
At least one NextSeq run produced a small negative value for y coordinate (-5), so allow small negative values and see what happens.
MIN_Q - Variable in class picard.sam.FastqToSam
 
MIN_QD - Variable in class picard.vcf.filter.FilterVcf
 
MINIMUM_BAITS_PER_TARGET - Variable in class picard.util.BaitDesigner
 
MINIMUM_BASE_QUALITY - Variable in class picard.analysis.CollectRawWgsMetrics
 
MINIMUM_BASE_QUALITY - Variable in class picard.analysis.CollectWgsMetrics
 
MINIMUM_BASE_QUALITY - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
MINIMUM_DISTANCE - Variable in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
 
MINIMUM_GENOME_FRACTION - Variable in class picard.analysis.CollectGcBiasMetrics
 
MINIMUM_INSERT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
MINIMUM_INSERT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
 
MINIMUM_LENGTH - Variable in class picard.analysis.CollectRnaSeqMetrics
 
MINIMUM_LOD_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectJumpingLibraryMetrics
 
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectOxoGMetrics
 
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectRawWgsMetrics
 
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectWgsMetrics
 
MINIMUM_MAPPING_QUALITY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
MINIMUM_PCT - Variable in class picard.analysis.CollectInsertSizeMetrics
 
MINIMUM_QUALITY - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
MINIMUM_QUALITY - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
MINIMUM_QUALITY - Variable in class picard.illumina.IlluminaBasecallsToSam
 
MINIMUM_QUALITY_SCORE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
MINIMUM_QUALITY_SCORE - Variable in class picard.analysis.CollectOxoGMetrics
 
MINIMUM_READ_LENGTH - Variable in class picard.analysis.CollectRrbsMetrics
 
MISSING_SITES_HOM_REF - Variable in class picard.vcf.GenotypeConcordance
 
MMapBackedIteratorFactory - Class in picard.illumina.parser.readers
MMapBackedIteratorFactory a file reader that takes a header size and a binary file, maps the file to a read-only byte buffer and provides methods to retrieve the header as it's own bytebuffer and create iterators of different data types over the values of file (starting after the end of the header).
MMapBackedIteratorFactory() - Constructor for class picard.illumina.parser.readers.MMapBackedIteratorFactory
 
MODE - Variable in class picard.sam.ValidateSamFile
 
MOLECULAR_BARCODE_NAME - Variable in class picard.illumina.IlluminaBasecallingMetrics
The barcode name for which the metrics were calculated.
MOLECULAR_BARCODE_SEQUENCE_1 - Variable in class picard.illumina.IlluminaBasecallingMetrics
The barcode sequence for which the metrics were calculated.
MostDistantPrimaryAlignmentSelectionStrategy - Class in picard.sam
For a paired-end aligner that aligns each end independently, select the pair of alignments that result in the largest insert size.
MostDistantPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
 
MultiLevelCollector<METRIC_TYPE extends MetricBase,Histogram_KEY extends Comparable,ARGTYPE> - Class in picard.metrics
MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP).
MultiLevelCollector() - Constructor for class picard.metrics.MultiLevelCollector
 
MultilevelMetrics - Class in picard.metrics
 
MultilevelMetrics() - Constructor for class picard.metrics.MultilevelMetrics
 
MULTIPLEX_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
multiply(double[], double[]) - Static method in class picard.util.MathUtil
Calculates the product of two arrays of the same length.
multithreadingBy(int) - Method in class picard.vcf.processor.VariantProcessor.Builder
 
MultiTileBclFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
MultiTileBclFileFaker() - Constructor for class picard.illumina.parser.fakers.MultiTileBclFileFaker
 
MultiTileBclFileUtil - Class in picard.illumina.parser
NextSeq-style bcl's have all tiles for a cycle in a single file.
MultiTileBclParser - Class in picard.illumina.parser
Parse .bcl.bgzf files that contain multiple tiles in a single file.
MultiTileBclParser(File, int, CycleIlluminaFileMap, OutputMapping, boolean, BclQualityEvaluationStrategy, TileIndex) - Constructor for class picard.illumina.parser.MultiTileBclParser
 
MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
For file types for which there is one file per lane, with fixed record size, and all the tiles in it, so the s_.bci file can be used to figure out where each tile starts and ends.
MultiTileFilterParser - Class in picard.illumina.parser
Read filter file that contains multiple tiles in a single file.
MultiTileFilterParser(TileIndex, List<Integer>, File) - Constructor for class picard.illumina.parser.MultiTileFilterParser
 
MultiTileLocsFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
MultiTileLocsFileFaker() - Constructor for class picard.illumina.parser.fakers.MultiTileLocsFileFaker
 
MultiTileLocsParser - Class in picard.illumina.parser
Read locs file that contains multiple tiles in a single file.
MultiTileLocsParser(TileIndex, List<Integer>, File, int) - Constructor for class picard.illumina.parser.MultiTileLocsParser
 
MultiTileParser<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
Abstract class for files with fixed-length records for multiple tiles, e.g.
MultiTileParser(TileIndex, List<Integer>, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.MultiTileParser
 

N

N_CYCLES - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
NA - Static variable in class picard.vcf.GenotypeConcordanceScheme
These are convenience variables for defining a scheme.
name - Variable in class picard.annotation.Gene.Transcript
 
NAME - Variable in class picard.util.FifoBuffer
 
NATURAL_LOG_MATH - Static variable in class picard.util.MathUtil
 
NEAR_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of PF aligned bases that mapped to within a fixed interval of an amplified region, but not on a baited region.
NEAR_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region.
needsReferenceSequence() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
 
NestedOptions - Annotation Type in picard.cmdline
Used to annotate a field in a CommandLineProgram that holds a instance containing @Option-annotated fields.
NEW_SAMPLE_NAME - Variable in class picard.vcf.RenameSampleInVcf
 
next() - Method in class picard.illumina.parser.IlluminaDataProvider
 
next() - Method in class picard.illumina.parser.MultiTileParser
 
next() - Method in class picard.illumina.parser.PerTileParser
 
next() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
Return the next set of coordinates in a given file.
next() - Method in class picard.illumina.parser.readers.BarcodeFileReader
 
next() - Method in class picard.illumina.parser.readers.BclReader
 
next() - Method in class picard.illumina.parser.readers.FilterFileReader
 
next() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
 
next() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
next() - Method in class picard.util.AsyncIterator
 
next() - Method in interface picard.util.AtomicIterator
Produces the next element from the iterator, if there is one; otherwise, produces Optional.Absent
next() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
next() - Method in class picard.vcf.ByIntervalListVariantContextIterator
 
next() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
Provides the next record from the underlying iterator after applying filter strings generated by the set of filters in use by the iterator.
next() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
 
NEXT_BASE_QUALITY_THRESHOLD - Variable in class picard.analysis.CollectRrbsMetrics
 
NO_LIBRARIES_SPECIFIED_IN_HEADER - Static variable in class picard.sam.SplitSamByLibrary
 
NO_MATCH - Static variable in class picard.util.ClippingUtility
The value returned by methods returning int when no match is found.
NO_PHENO - Static variable in class picard.pedigree.PedFile
 
NON_CPG_BASES - Variable in class picard.analysis.RrbsSummaryMetrics
Number of times a non-CpG cytosine was encountered
NON_CPG_CONVERTED_BASES - Variable in class picard.analysis.RrbsSummaryMetrics
Number of times a non-CpG cytosine was converted (C->T for +, G->A for -)
NON_REF_GENOTYPE_CONCORDANCE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The non-ref genotype concordance, ie for all var states only.
None - Class in picard.cmdline.programgroups
 
None() - Constructor for class picard.cmdline.programgroups.None
 
NONJUMP_DUPLICATE_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of inward-facing pais that are duplicates
NONJUMP_DUPLICATE_PCT - Variable in class picard.analysis.JumpingLibraryMetrics
The percentage of inward-facing pairs that are marked as duplicates
NONJUMP_LIBRARY_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
The estimated library size for inward-facing pairs
NONJUMP_MEAN_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
The mean insert size for inward-facing pairs
NONJUMP_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of inward-facing pairs in the SAM file
NONJUMP_STDEV_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
The standard deviation on the insert size for inward-facing pairs
nonSkips - Variable in class picard.illumina.parser.ReadStructure
 
NORMALIZED_COVERAGE - Variable in class picard.analysis.GcBiasDetailMetrics
The ration of "coverage" in this GC bin vs.
NormalizeFasta - Class in picard.reference
Little program to "normalize" a fasta file to ensure that all line of sequence are the same length, and are a reasonable length!
NormalizeFasta() - Constructor for class picard.reference.NormalizeFasta
 
NOVEL_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of high confidence Indels called that were not found in dbSNP
NOVEL_INS_DEL_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The Insertion/Deletion ratio of the Indel calls made at non-dbSNP sites
NOVEL_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of high confidence SNPS called that were not found in dbSNP
NOVEL_TITV - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The Transition/Transversion ratio of the SNP calls made at non-dbSNP sites
NUM_ADAPTERS_TO_KEEP - Variable in class picard.illumina.MarkIlluminaAdapters
 
NUM_CHANNELS - Static variable in enum picard.illumina.parser.IntensityChannel
 
NUM_IN_DB_SNP - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of high confidence SNPs found in dbSNP
NUM_IN_DB_SNP_COMPLEX_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of high confidence complex Indels found in dbSNP
NUM_IN_DB_SNP_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of high confidence Indels found in dbSNP
NUM_IN_DB_SNP_MULTIALLELIC - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of high confidence multiallelic SNPs found in dbSNP
NUM_N - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
 
NUM_PROCESSORS - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
NUM_PROCESSORS - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
NUM_PROCESSORS - Variable in class picard.illumina.IlluminaBasecallsToSam
 
NUM_PROCESSORS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
NUM_Q_GT_TWO - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
 
NUM_SEQUENCES - Variable in class picard.sam.CreateSequenceDictionary
 
NUM_SINGLETONS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
For summary metrics, the number of variants that appear in only one sample.
numClusters - Variable in class picard.illumina.parser.readers.FilterFileReader
The number of cluster's pf values stored in this file
numOutputReads() - Method in class picard.illumina.parser.OutputMapping
 

O

OFF_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of PF aligned bases that mapped to neither on or near an amplicon.
OFF_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
The number of PF aligned bases that mapped to neither on or near a bait.
OLD_SAMPLE_NAME - Variable in class picard.vcf.RenameSampleInVcf
 
ON_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of PF aligned amplified that mapped to an amplified region of the genome.
ON_AMPLICON_VS_SELECTED - Variable in class picard.analysis.directed.TargetedPcrMetrics
The percentage of on+near amplicon bases that are on as opposed to near.
ON_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
The number of PF aligned bases that mapped to a baited region of the genome.
ON_BAIT_VS_SELECTED - Variable in class picard.analysis.directed.HsMetrics
The percentage of on+near bait bases that are on as opposed to near.
ON_TARGET_BASES - Variable in class picard.analysis.directed.HsMetrics
The number of PF aligned bases that mapped to a targeted region of the genome.
ON_TARGET_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of PF aligned bases that mapped to a targeted region of the genome.
ON_TARGET_FROM_PAIR_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of PF aligned bases that are mapped in pair to a targeted region of the genome.
ONE_MISMATCH_MATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
The number of all reads matching this barcode that matched with 1 error or no-call.
openInputs() - Method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
Since this may read it's inputs more than once this method does all the opening and checking of the inputs.
OPTICAL_DUPLICATE_PIXEL_DISTANCE - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
opticalDuplicateFinder - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
OpticalDuplicateFinder - Class in picard.sam.markduplicates.util
Contains methods for finding optical duplicates.
OpticalDuplicateFinder() - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
OpticalDuplicateFinder(int) - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
OpticalDuplicateFinder(String) - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
OpticalDuplicateFinder(String, int) - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
OpticalDuplicateFinder(String, int, Log) - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
OpticalDuplicateFinder.PhysicalLocation - Interface in picard.sam.markduplicates.util
Small interface that provides access to the physical location information about a cluster.
opticalDuplicatePixelDistance - Variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
Option - Annotation Type in picard.cmdline
Used to annotate which fields of a CommandLineProgram are options given at the command line.
optionLength(String) - Static method in class picard.util.MetricsDoclet
Required method by the javadoc caller that returns the expected number of elements for doclet specific command line arguments.
orientation - Variable in class picard.sam.markduplicates.util.ReadEnds
 
orientationForOpticalDuplicates - Variable in class picard.sam.markduplicates.util.ReadEnds
For optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate
out - Variable in class picard.sam.FixMateInformation
 
OUTPUT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
 
OUTPUT - Variable in class picard.analysis.CollectMultipleMetrics
 
OUTPUT - Variable in class picard.analysis.CollectOxoGMetrics
 
OUTPUT - Variable in class picard.analysis.CollectQualityYieldMetrics
 
OUTPUT - Variable in class picard.analysis.CollectWgsMetrics
 
OUTPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
OUTPUT - Variable in class picard.analysis.SinglePassSamProgram
 
OUTPUT - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
 
OUTPUT - Variable in class picard.illumina.IlluminaBasecallsToSam
 
OUTPUT - Variable in class picard.illumina.MarkIlluminaAdapters
 
OUTPUT - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
OUTPUT - Variable in class picard.reference.ExtractSequences
 
OUTPUT - Variable in class picard.reference.NormalizeFasta
 
OUTPUT - Variable in class picard.sam.AddCommentsToBam
 
OUTPUT - Variable in class picard.sam.AddOrReplaceReadGroups
 
OUTPUT - Variable in class picard.sam.BuildBamIndex
 
OUTPUT - Variable in class picard.sam.CalculateReadGroupChecksum
 
OUTPUT - Variable in class picard.sam.CleanSam
 
OUTPUT - Variable in class picard.sam.CreateSequenceDictionary
 
OUTPUT - Variable in class picard.sam.DownsampleSam
 
OUTPUT - Variable in class picard.sam.FastqToSam
 
OUTPUT - Variable in class picard.sam.FilterSamReads
 
OUTPUT - Variable in class picard.sam.FixMateInformation
 
OUTPUT - Variable in class picard.sam.GatherBamFiles
 
OUTPUT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
OUTPUT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
OUTPUT - Variable in class picard.sam.MergeBamAlignment
 
OUTPUT - Variable in class picard.sam.MergeSamFiles
 
OUTPUT - Variable in class picard.sam.PositionBasedDownsampleSam
 
OUTPUT - Variable in class picard.sam.ReorderSam
 
OUTPUT - Variable in class picard.sam.ReplaceSamHeader
 
OUTPUT - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
OUTPUT - Variable in class picard.sam.RevertSam
 
OUTPUT - Variable in class picard.sam.SamFormatConverter
 
OUTPUT - Variable in class picard.sam.SortSam
 
OUTPUT - Variable in class picard.sam.SplitSamByLibrary
 
OUTPUT - Variable in class picard.sam.ValidateSamFile
 
OUTPUT - Variable in class picard.util.BedToIntervalList
 
OUTPUT - Variable in class picard.util.IntervalListTools
 
OUTPUT - Variable in class picard.util.LiftOverIntervalList
 
OUTPUT - Variable in class picard.util.ScatterIntervalsByNs
 
OUTPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
 
OUTPUT - Variable in class picard.vcf.filter.FilterVcf
 
OUTPUT - Variable in class picard.vcf.GatherVcfs
 
OUTPUT - Variable in class picard.vcf.GenotypeConcordance
 
OUTPUT - Variable in class picard.vcf.LiftoverVcf
 
OUTPUT - Variable in class picard.vcf.MakeSitesOnlyVcf
 
OUTPUT - Variable in class picard.vcf.MergeVcfs
 
OUTPUT - Variable in class picard.vcf.RenameSampleInVcf
 
OUTPUT - Variable in class picard.vcf.SortVcf
 
OUTPUT - Variable in class picard.vcf.UpdateVcfSequenceDictionary
 
OUTPUT - Variable in class picard.vcf.VcfFormatConverter
 
OUTPUT - Variable in class picard.vcf.VcfToIntervalList
 
OUTPUT_AGILENT_FILES - Variable in class picard.util.BaitDesigner
 
OUTPUT_ALL_ROWS - Variable in class picard.vcf.GenotypeConcordance
 
OUTPUT_BASE - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 
OUTPUT_DIR - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
OUTPUT_DIR - Variable in class picard.sam.SamToFastq
 
OUTPUT_DIRECTORY - Variable in class picard.illumina.CollectIlluminaLaneMetrics
 
OUTPUT_DIRECTORY - Variable in class picard.util.BaitDesigner
 
OUTPUT_FILE_PREFIX - Variable in class picard.fastq.BamToBfq
 
OUTPUT_PER_RG - Variable in class picard.sam.SamToFastq
 
OUTPUT_PREFIX - Variable in class picard.illumina.CollectIlluminaLaneMetrics
 
OUTPUT_PREFIX - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
OUTPUT_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
OUTPUT_TYPE - Variable in class picard.util.ScatterIntervalsByNs
 
OutputMapping - Class in picard.illumina.parser
In multiple locations we need to know what cycles are output, as of now we output all non-skip cycles, but rather than sprinkle this knowledge throughout the parser code, instead OutputMapping provides all the data a client might want about the cycles to be output including what ReadType they are.
OutputMapping(ReadStructure) - Constructor for class picard.illumina.parser.OutputMapping
Create an OutputMapping from a readStructure, currently the outputSubstructure just references the readStructure.nonSkips Substructure
OXIDATION_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASES
OXIDATION_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-10 * log10(OXIDATION_ERROR_RATE)

P

PADDING - Variable in class picard.util.BaitDesigner
 
PADDING - Variable in class picard.util.IntervalListTools
 
PAIR_ORIENTATION - Variable in class picard.analysis.InsertSizeMetrics
The pair orientation of the reads in this data category.
PAIRED_RUN - Variable in class picard.fastq.BamToBfq
 
PAIRED_RUN - Variable in class picard.illumina.MarkIlluminaAdapters
 
PAIRED_RUN - Variable in class picard.sam.MergeBamAlignment
Deprecated.
PARAMETER_DOC - Static variable in class picard.illumina.parser.ReadStructure
 
ParameterizedFileUtil - Class in picard.illumina.parser
 
ParameterizedFileUtil(boolean, String, File, FileFaker, int, boolean) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
 
ParameterizedFileUtil(boolean, String, File, FileFaker, int) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
 
ParameterizedFileUtil(String, String, File, FileFaker, int) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
 
parseArgs(String[]) - Method in class picard.cmdline.CommandLineProgram
 
parseOptions(PrintStream, String[]) - Method in class picard.cmdline.CommandLineParser
Parse command-line options, and store values in callerOptions object passed to ctor.
parseOptionsFile(String, boolean) - Method in class picard.cmdline.CommandLineParser
 
parseTileMetrics(File, ReadStructure) - Static method in class picard.illumina.parser.TileMetricsUtil
Returns an unmodifiable collection of tile data read from the provided file.
PASS_FILTER - Static variable in class picard.vcf.filter.FilterApplyingVariantIterator
The "PASS"ing filter String.
PCT_100X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 100X sequence coverage in post-filtering bases.
PCT_10X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 10X sequence coverage in post-filtering bases.
PCT_15X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 15X sequence coverage in post-filtering bases.
PCT_20X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 20X sequence coverage in post-filtering bases.
PCT_25X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 25X sequence coverage in post-filtering bases.
PCT_30X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 30X sequence coverage in post-filtering bases.
PCT_40X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 40X sequence coverage in post-filtering bases.
PCT_50X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 50X sequence coverage in post-filtering bases.
PCT_5X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.
PCT_60X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 60X sequence coverage in post-filtering bases.
PCT_70X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 70X sequence coverage in post-filtering bases.
PCT_80X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 80X sequence coverage in post-filtering bases.
PCT_90X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 90X sequence coverage in post-filtering bases.
PCT_A - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
PCT_ADAPTER - Variable in class picard.analysis.AlignmentSummaryMetrics
The percentage of PF reads that are unaligned and match to a known adapter sequence right from the start of the read.
PCT_AMPLIFIED_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
On+Near Amplicon Bases / PF Bases Aligned.
PCT_C - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
PCT_CHIMERAS - Variable in class picard.analysis.AlignmentSummaryMetrics
The percentage of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.
PCT_CHIMERAS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of chimeric pairs expressed as a percentage of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
PCT_CODING_BASES - Variable in class picard.analysis.RnaSeqMetrics
CODING_BASES / PF_ALIGNED_BASES
PCT_CONVERTED - Variable in class picard.analysis.RrbsCpgDetailMetrics
TOTAL_BASES / CONVERTED_BASES
PCT_CORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
CORRECT_STRAND_READS/(CORRECT_STRAND_READS + INCORRECT_STRAND_READS).
PCT_CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
CPG_BASES_SEEN / CPG_BASES_CONVERTED
PCT_DBSNP - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The percentage of high confidence SNPs in dbSNP
PCT_DBSNP_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The percentage of high confidence Indels in dbSNP
PCT_EXC_BASEQ - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of aligned bases that were filtered out because they were of low base quality (default is < 20).
PCT_EXC_CAPPED - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of aligned bases that were filtered out because they would have raised coverage above the capped value (default cap = 250x).
PCT_EXC_DUPE - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
PCT_EXC_MAPQ - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (default is < 20).
PCT_EXC_OVERLAP - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
PCT_EXC_TOTAL - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The total fraction of aligned bases excluded due to all filters.
PCT_EXC_UNPAIRED - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.
PCT_G - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
PCT_INTERGENIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
INTERGENIC_BASES / PF_ALIGNED_BASES
PCT_INTRONIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
INTRONIC_BASES / PF_ALIGNED_BASES
PCT_JUMPS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of outward-facing pairs expressed as a percentage of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
PCT_MATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
The percentage of all reads in the lane that matched to this barcode.
PCT_MRNA_BASES - Variable in class picard.analysis.RnaSeqMetrics
PCT_UTR_BASES + PCT_CODING_BASES
PCT_N - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
PCT_NON_CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
NON_CPG_BASES / NON_CPG_CONVERTED_BASES
PCT_NONJUMPS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of inward-facing pairs expressed as a percentage of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
PCT_OFF_AMPLICON - Variable in class picard.analysis.directed.TargetedPcrMetrics
The percentage of aligned PF bases that mapped neither on or near an amplicon.
PCT_OFF_BAIT - Variable in class picard.analysis.directed.HsMetrics
The percentage of aligned PF bases that mapped neither on or near a bait.
PCT_PF_FAIL_EMPTY - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads).
PCT_PF_FAIL_MISALIGNED - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads).
PCT_PF_FAIL_POLYCLONAL - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads).
PCT_PF_FAIL_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The fraction of PF_READS
PCT_PF_FAIL_UNKNOWN - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads).
PCT_PF_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
The percentage of reads that are PF (PF_READS / TOTAL_READS)
PCT_PF_READS - Variable in class picard.analysis.directed.HsMetrics
PF reads / total reads.
PCT_PF_READS - Variable in class picard.analysis.directed.TargetedPcrMetrics
PF reads / total reads.
PCT_PF_READS_ALIGNED - Variable in class picard.analysis.AlignmentSummaryMetrics
The percentage of PF reads that aligned to the reference sequence.
PCT_PF_UQ_READS - Variable in class picard.analysis.directed.HsMetrics
PF Unique Reads / Total Reads.
PCT_PF_UQ_READS - Variable in class picard.analysis.directed.TargetedPcrMetrics
PF Unique Reads / Total Reads.
PCT_PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.HsMetrics
PF Reads Aligned / PF Reads.
PCT_PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.TargetedPcrMetrics
PF Reads Aligned / PF Reads.
PCT_READS_ALIGNED_IN_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
The percentage of reads whose mate pair was also aligned to the reference.
PCT_RIBOSOMAL_BASES - Variable in class picard.analysis.RnaSeqMetrics
RIBOSOMAL_BASES / PF_ALIGNED_BASES
PCT_SELECTED_BASES - Variable in class picard.analysis.directed.HsMetrics
On+Near Bait Bases / PF Bases Aligned.
PCT_T - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
PCT_TARGET_BASES_100X - Variable in class picard.analysis.directed.HsMetrics
The percentage of ALL target bases achieving 100X or greater coverage.
PCT_TARGET_BASES_10X - Variable in class picard.analysis.directed.HsMetrics
The percentage of ALL target bases achieving 10X or greater coverage.
PCT_TARGET_BASES_10X - Variable in class picard.analysis.directed.TargetedPcrMetrics
The percentage of ALL target bases achieving 10X or greater coverage.
PCT_TARGET_BASES_20X - Variable in class picard.analysis.directed.HsMetrics
The percentage of ALL target bases achieving 20X or greater coverage.
PCT_TARGET_BASES_20X - Variable in class picard.analysis.directed.TargetedPcrMetrics
The percentage of ALL target bases achieving 20X or greater coverage.
PCT_TARGET_BASES_2X - Variable in class picard.analysis.directed.HsMetrics
The percentage of ALL target bases achieving 2X or greater coverage.
PCT_TARGET_BASES_2X - Variable in class picard.analysis.directed.TargetedPcrMetrics
The percentage of ALL target bases achieving 2X or greater coverage.
PCT_TARGET_BASES_30X - Variable in class picard.analysis.directed.HsMetrics
The percentage of ALL target bases achieving 30X or greater coverage.
PCT_TARGET_BASES_30X - Variable in class picard.analysis.directed.TargetedPcrMetrics
The percentage of ALL target bases achieving 30X or greater coverage.
PCT_TARGET_BASES_40X - Variable in class picard.analysis.directed.HsMetrics
The percentage of ALL target bases achieving 40X or greater coverage.
PCT_TARGET_BASES_50X - Variable in class picard.analysis.directed.HsMetrics
The percentage of ALL target bases achieving 50X or greater coverage.
PCT_USABLE_BASES - Variable in class picard.analysis.RnaSeqMetrics
The percentage of bases mapping to mRNA divided by the total number of PF bases.
PCT_USABLE_BASES_ON_BAIT - Variable in class picard.analysis.directed.HsMetrics
The number of aligned, de-duped, on-bait bases out of the PF bases available.
PCT_USABLE_BASES_ON_TARGET - Variable in class picard.analysis.directed.HsMetrics
The number of aligned, de-duped, on-target bases out of the PF bases available.
PCT_UTR_BASES - Variable in class picard.analysis.RnaSeqMetrics
UTR_BASES / PF_ALIGNED_BASES
PDF_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
 
PedFile - Class in picard.pedigree
Represents a .ped file of family information as documented here: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml Stores the information in memory as a map of individualId -> Pedigree information for that individual
PedFile(boolean) - Constructor for class picard.pedigree.PedFile
 
PedFile.PedTrio - Class in picard.pedigree
 
PedFile.PedTrio(String, String, String, String, Sex, Number) - Constructor for class picard.pedigree.PedFile.PedTrio
Constructs a TRIO that cannot be modified after the fact.
peek() - Method in class picard.sam.markduplicates.util.MarkQueue
Returns the first element in this queue
PER_TARGET_COVERAGE - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
PER_TILE_PATTERN_STRING - Static variable in class picard.illumina.parser.ParameterizedFileUtil
 
PERCENT_DUPLICATION - Variable in class picard.sam.DuplicationMetrics
The percentage of mapped sequence that is marked as duplicate.
percentageOrNull(Long, Long) - Static method in class picard.util.MathUtil
Obtains percentage of two Longs
PERFECT_MATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
The number of all reads matching this barcode that matched with 0 errors or no-calls.
PerTileFileUtil - Class in picard.illumina.parser
 
PerTileFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTileFileUtil
 
PerTileFileUtil(String, File, FileFaker, int, boolean) - Constructor for class picard.illumina.parser.PerTileFileUtil
 
PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
Abstract base class for Parsers that open a single tile file at a time and iterate through them.
PerTileParser(IlluminaFileMap) - Constructor for class picard.illumina.parser.PerTileParser
 
PerTileParser(IlluminaFileMap, int) - Constructor for class picard.illumina.parser.PerTileParser
 
PerTilePerCycleFileUtil - Class in picard.illumina.parser
 
PerTilePerCycleFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTilePerCycleFileUtil
 
PerUnitMetricCollector<BEAN extends MetricBase,HKEY extends Comparable,ARGTYPE> - Interface in picard.metrics
PerRecordCollector - An interface for classes that collect data in order to generate one or more metrics.
PF_ALIGNED_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.
PF_ALIGNED_BASES - Variable in class picard.analysis.RnaSeqMetrics
The total number of aligned PF bases.
PF_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The total number of bases in all PF reads
PF_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
THe number of bases in the SAM or BAM file to be examined
PF_BASES - Variable in class picard.analysis.RnaSeqMetrics
The total number of PF bases including non-aligned reads.
PF_BASES - Variable in class picard.illumina.IlluminaBasecallingMetrics
The total number of passing-filter bases assigned to the index.
PF_CLUSTERS - Variable in class picard.illumina.IlluminaBasecallingMetrics
The total number of PF clusters assigned to the index.
PF_FAIL_EMPTY - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile that are deemed empty.
PF_FAIL_MISALIGNED - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile that are deemed "misaligned".
PF_FAIL_POLYCLONAL - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile that are deemed multiclonal.
PF_FAIL_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile.
PF_FAIL_UNKNOWN - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile that have not been classified.
PF_HQ_ALIGNED_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of bases aligned to the reference sequence in reads that were mapped at high quality.
PF_HQ_ALIGNED_Q20_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher.
PF_HQ_ALIGNED_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of PF reads that were aligned to the reference sequence with a mapping quality of Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the alignment is wrong.
PF_HQ_ERROR_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
The percentage of bases that mismatch the reference in PF HQ aligned reads.
PF_HQ_MEDIAN_MISMATCHES - Variable in class picard.analysis.AlignmentSummaryMetrics
The median number of mismatches versus the reference sequence in reads that were aligned to the reference at high quality (i.e.
PF_INDEL_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of insertion and deletion events per 100 aligned bases.
PF_MISMATCH_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
The rate of bases mismatching the reference for all bases aligned to the reference sequence.
PF_NOISE_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of PF reads that are marked as noise reads.
PF_NORMALIZED_MATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
The "normalized" matches to each barcode.
PF_ONE_MISMATCH_MATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
The number of PF reads matching this barcode that matched with 1 error or no-call.
PF_PCT_MATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
The percentage of PF reads in the lane that matched to this barcode.
PF_PERFECT_MATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
The number of PF reads matching this barcode that matched with 0 errors or no-calls.
PF_Q20_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The number of bases in PF reads that achieve quality score 20 or higher
PF_Q20_EQUIVALENT_YIELD - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The sum of quality scores of all bases divided by 20
PF_Q30_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The number of bases in PF reads that achieve quality score 20 or higher
PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
The rate of PF reads matching this barcode to PF reads matching the most prevelant barcode.
PF_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of PF reads where PF is defined as passing Illumina's filter.
PF_READS - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The number of reads that are PF - pass filter
PF_READS - Variable in class picard.analysis.directed.HsMetrics
The number of reads that pass the vendor's filter.
PF_READS - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of reads that pass the vendor's filter.
PF_READS - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
The number of PF reads matching this barcode (always less than or equal to READS).
PF_READS - Variable in class picard.illumina.IlluminaBasecallingMetrics
The total number of passing-filter reads assigned to the index.
PF_READS_ALIGNED - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of PF reads that were aligned to the reference sequence.
PF_READS_ONLY - Variable in class picard.analysis.CollectBaseDistributionByCycle
 
PF_READS_ONLY - Variable in class picard.analysis.MeanQualityByCycle
 
PF_READS_ONLY - Variable in class picard.analysis.QualityScoreDistribution
 
PF_READS_ONLY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
PF_SELECTED_PAIRS - Variable in class picard.analysis.directed.TargetedPcrMetrics
Tracks the number of read pairs that we see that are PF (used to calculate library size)
PF_SELECTED_UNIQUE_PAIRS - Variable in class picard.analysis.directed.TargetedPcrMetrics
Tracks the number of unique PF reads pairs we see (used to calc library size)
PF_STATUS - Variable in class picard.sam.ViewSam
 
PF_UNIQUE_READS - Variable in class picard.analysis.directed.HsMetrics
The number of PF reads that are not marked as duplicates.
PF_UNIQUE_READS - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of PF reads that are not marked as duplicates.
PF_UQ_BASES_ALIGNED - Variable in class picard.analysis.directed.HsMetrics
The number of bases in the PF aligned reads that are mapped to a reference base.
PF_UQ_BASES_ALIGNED - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.HsMetrics
The number of PF unique reads that are aligned with mapping score > 0 to the reference genome.
PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of PF unique reads that are aligned with mapping score > 0 to the reference genome.
PG_PROGRAM_NAME - Static variable in class picard.sam.PositionBasedDownsampleSam
 
pgIdsSeen - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
The program groups that have been seen during the course of examining the input records.
PHASING_APPLIED - Variable in class picard.illumina.IlluminaPhasingMetrics
 
PhysicalLocation - Class in picard.sam.util
Small interface that provides access to the physical location information about a cluster.
PhysicalLocation() - Constructor for class picard.sam.util.PhysicalLocation
 
PhysicalLocation(String) - Constructor for class picard.sam.util.PhysicalLocation
 
PhysicalLocationForMateCigar - Class in picard.sam.markduplicates.util
Stores the minimal information needed for optical duplicate detection.
PhysicalLocationForMateCigar(OpticalDuplicateFinder.PhysicalLocation) - Constructor for class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
PhysicalLocationForMateCigarSet - Class in picard.sam.markduplicates.util
This stores records that are comparable for detecting optical duplicates.
PhysicalLocationForMateCigarSet() - Constructor for class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
 
picard - package picard
 
picard.analysis - package picard.analysis
 
picard.analysis.artifacts - package picard.analysis.artifacts
 
picard.analysis.directed - package picard.analysis.directed
 
picard.annotation - package picard.annotation
 
picard.cmdline - package picard.cmdline
 
picard.cmdline.programgroups - package picard.cmdline.programgroups
 
picard.fastq - package picard.fastq
 
picard.illumina - package picard.illumina
 
picard.illumina.parser - package picard.illumina.parser
 
picard.illumina.parser.fakers - package picard.illumina.parser.fakers
 
picard.illumina.parser.readers - package picard.illumina.parser.readers
 
picard.illumina.quality - package picard.illumina.quality
 
picard.metrics - package picard.metrics
 
picard.pedigree - package picard.pedigree
 
picard.reference - package picard.reference
 
picard.sam - package picard.sam
 
picard.sam.markduplicates - package picard.sam.markduplicates
 
picard.sam.markduplicates.util - package picard.sam.markduplicates.util
 
picard.sam.util - package picard.sam.util
 
picard.util - package picard.util
 
picard.vcf - package picard.vcf
 
picard.vcf.filter - package picard.vcf.filter
 
picard.vcf.processor - package picard.vcf.processor
 
picard.vcf.processor.util - package picard.vcf.processor.util
 
PicardCommandLine - Class in picard.cmdline
This is the main class of Picard and is the way of executing individual command line programs.
PicardCommandLine() - Constructor for class picard.cmdline.PicardCommandLine
 
PicardException - Exception in picard
Basic Picard runtime exception that, for now, does nothing much
PicardException(String) - Constructor for exception picard.PicardException
 
PicardException(String, Throwable) - Constructor for exception picard.PicardException
 
pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.BestEndMapqPrimaryAlignmentStrategy
Primary alignment was filtered out.
pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.BestMapqPrimaryAlignmentSelectionStrategy
Primary alignment was filtered out.
pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy
 
pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
 
pickPrimaryAlignment(HitsForInsert) - Method in interface picard.sam.PrimaryAlignmentSelectionStrategy
When this method returns, one alignment has been marked as primary according to the implementation's strategy.
PLATFORM - Variable in class picard.illumina.IlluminaBasecallsToSam
 
PLATFORM - Variable in class picard.sam.FastqToSam
 
PLATFORM_MODEL - Variable in class picard.sam.FastqToSam
 
PLATFORM_UNIT - Variable in class picard.sam.FastqToSam
 
pNormalizeLogProbability(double[]) - Static method in class picard.util.MathUtil
Takes a complete set of mutually exclusive logPosteriors and converts them to probabilities that sum to 1 with as much fidelity as possible.
pNormalizeVector(double[]) - Static method in class picard.util.MathUtil
Takes a vector of numbers and converts it to a vector of probabilities that sum to 1 with as much fidelity as possible.
poll(SamRecordTrackingBuffer, SAMFileHeader, OpticalDuplicateFinder, LibraryIdGenerator) - Method in class picard.sam.markduplicates.util.MarkQueue
The poll method will return the read end that is *not* the duplicate of all comparable read ends that have been seen.
POOL_SIZE - Variable in class picard.util.BaitDesigner
 
PosFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
PosFileFaker() - Constructor for class picard.illumina.parser.fakers.PosFileFaker
 
PosFileReader - Class in picard.illumina.parser.readers
The pos file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
PosFileReader(File) - Constructor for class picard.illumina.parser.readers.PosFileReader
 
POSITION - Variable in class picard.analysis.RrbsCpgDetailMetrics
Position within the sequence of the CpG site
PositionalArguments - Annotation Type in picard.cmdline
Used to annotate which field of a CommandLineProgram should store parameters given at the command line which are not options.
PositionBasedDownsampleSam - Class in picard.sam
Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither end of the pair.
PositionBasedDownsampleSam() - Constructor for class picard.sam.PositionBasedDownsampleSam
 
PosParser - Class in picard.illumina.parser
PosParser parses multiple files formatted as one of the three file formats that contain position information only (pos, locs, and clocs).
PosParser(IlluminaFileMap, IlluminaFileUtil.SupportedIlluminaFormat) - Constructor for class picard.illumina.parser.PosParser
 
PosParser(IlluminaFileMap, int, IlluminaFileUtil.SupportedIlluminaFormat) - Constructor for class picard.illumina.parser.PosParser
 
Ppv(GenotypeConcordanceScheme, GenotypeConcordanceStates.CallState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the PPV defined by the scheme across the subset of call states.
PRE_ADAPTER_DETAILS_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
 
PRE_ADAPTER_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
 
PredicateFilterDecoratingClosableIterator<T> - Class in picard.vcf.processor.util
Performs on-the-fly filtering of the provided VariantContext Iterator such that only variants that satisfy all predicates are emitted.
PredicateFilterDecoratingClosableIterator(CloseableIterator<T>, Collection<Predicate<T>>) - Constructor for class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
 
PREDICTED_INSERT_SIZE - Variable in class picard.sam.FastqToSam
 
PREPHASING_APPLIED - Variable in class picard.illumina.IlluminaPhasingMetrics
 
PRIMARY_ALIGNMENT_STRATEGY - Variable in class picard.sam.MergeBamAlignment
 
PrimaryAlignmentSelectionStrategy - Interface in picard.sam
Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever strategy is appropriate.
printUnknown(Set<Class<?>>, String) - Static method in class picard.cmdline.PicardCommandLine
When a command does not match any known command, searches for similar commands, using the same method as GIT
PRO_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact.
PRO_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact.
PROB_EXPLICIT_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
PROBABILITY - Variable in class picard.sam.DownsampleSam
 
process() - Method in class picard.vcf.processor.VariantProcessor
 
product(double...) - Method in class picard.util.MathUtil.LogMath
Computes the sum of the provided log values.
PROGRAM - Variable in class picard.analysis.CollectMultipleMetrics
 
PROGRAM_GROUP - Variable in class picard.sam.FastqToSam
 
PROGRAM_GROUP_COMMAND_LINE - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
PROGRAM_GROUP_COMMAND_LINE - Variable in class picard.sam.MergeBamAlignment
 
PROGRAM_GROUP_NAME - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
PROGRAM_GROUP_NAME - Variable in class picard.sam.MergeBamAlignment
 
PROGRAM_GROUP_VERSION - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
PROGRAM_GROUP_VERSION - Variable in class picard.sam.MergeBamAlignment
 
PROGRAM_RECORD_ID - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
PROGRAM_RECORD_ID - Variable in class picard.sam.MergeBamAlignment
 
PROGRAM_RECORD_ID_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
promote(int[]) - Static method in class picard.util.MathUtil
"Promotes" an int[] into a double array with the same values (or as close as precision allows).
PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN - Variable in class picard.illumina.MarkIlluminaAdapters
 
put(int, String, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
 
put(int, String, ReadEndsForMarkDuplicates) - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
Store the element in the map with the given key.

Q

Q20_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The number of bases in all reads that achieve quality score 20 or higher
Q20_EQUIVALENT_YIELD - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The sum of quality scores of all bases divided by 20
Q30_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The number of bases in all reads that achieve quality score 20 or higher
QdFilter - Class in picard.vcf.filter
Filters out sites that have a QD annotation applied to them and where the QD value is lower than a lower limit.
QdFilter(double) - Constructor for class picard.vcf.filter.QdFilter
 
QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
qualities - Variable in class picard.illumina.parser.BclData
 
QUALITY_FORMAT - Variable in class picard.sam.FastqToSam
 
QualityScoreDistribution - Class in picard.analysis
Charts quality score distribution within a BAM file.
QualityScoreDistribution() - Constructor for class picard.analysis.QualityScoreDistribution
 
QUIET - Variable in class picard.cmdline.CommandLineProgram
 

R

R - Static variable in class picard.sam.markduplicates.util.ReadEnds
 
RANDOM_SEED - Variable in class picard.sam.DownsampleSam
 
Range - Class in picard.illumina.parser
While structurally identical to CompositeIndex, this class is maintained as it makes code more readable when the two are used together (see QSeqParser)
Range(int, int) - Constructor for class picard.illumina.parser.Range
 
rapidParseInt(String) - Static method in class picard.sam.util.ReadNameParsingUtils
Very specialized method to rapidly parse a sequence of digits from a String up until the first non-digit character.
RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
The rate of all reads matching this barcode to all reads matching the most prevelant barcode.
RE_REVERSE - Variable in class picard.sam.SamToFastq
 
read(byte[], int, int) - Method in class picard.util.CircularByteBuffer
Read bytes from the buffer into the supplied array.
READ1_ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
 
READ1_MAX_BASES_TO_WRITE - Variable in class picard.sam.SamToFastq
 
READ1_TRIM - Variable in class picard.sam.MergeBamAlignment
 
READ1_TRIM - Variable in class picard.sam.SamToFastq
 
read1Coordinate - Variable in class picard.sam.markduplicates.util.ReadEnds
 
read1IndexInFile - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
read1ReferenceIndex - Variable in class picard.sam.markduplicates.util.ReadEnds
 
READ2_ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
 
READ2_MAX_BASES_TO_WRITE - Variable in class picard.sam.SamToFastq
 
READ2_TRIM - Variable in class picard.sam.MergeBamAlignment
 
READ2_TRIM - Variable in class picard.sam.SamToFastq
 
read2Coordinate - Variable in class picard.sam.markduplicates.util.ReadEnds
 
read2IndexInFile - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
read2ReferenceIndex - Variable in class picard.sam.markduplicates.util.ReadEnds
 
READ_CHUNK_SIZE - Variable in class picard.fastq.BamToBfq
 
READ_END - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
READ_GROUP - Variable in class picard.metrics.MultilevelMetrics
The read group to which these metrics apply.
READ_GROUP_ID - Variable in class picard.illumina.IlluminaBasecallsToSam
 
READ_GROUP_ID_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
READ_GROUP_NAME - Variable in class picard.sam.FastqToSam
 
READ_LENGTH - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The average read length of all the reads (will be fixed for a lane)
READ_LIST_FILE - Variable in class picard.sam.FilterSamReads
 
READ_NAME_FORMAT - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
READ_NAME_PREFIX - Variable in class picard.fastq.BamToBfq
 
READ_NAME_REGEX - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
READ_PAIR_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
The number of read pairs that were marked as duplicates.
READ_PAIR_OPTICAL_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
The number of read pairs duplicates that were caused by optical duplication.
READ_PAIRS - Variable in class picard.analysis.InsertSizeMetrics
The total number of read pairs that were examined in the entire distribution.
READ_PAIRS_EXAMINED - Variable in class picard.sam.DuplicationMetrics
The number of mapped read pairs examined.
READ_STARTS - Variable in class picard.analysis.GcBiasDetailMetrics
The number of reads whose start position is at the start of a window of this GC.
READ_STRUCTURE - Variable in class picard.illumina.CheckIlluminaDirectory
 
READ_STRUCTURE - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
 
READ_STRUCTURE - Variable in class picard.illumina.CollectIlluminaLaneMetrics
 
READ_STRUCTURE - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
READ_STRUCTURE - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
READ_STRUCTURE - Variable in class picard.illumina.IlluminaBasecallsToSam
 
ReadData - Class in picard.illumina.parser
Data for a single end of a paired-end read, a barcode read, or for the entire read if not paired end.
ReadData() - Constructor for class picard.illumina.parser.ReadData
 
ReadData(ReadType) - Constructor for class picard.illumina.parser.ReadData
 
ReadDescriptor - Class in picard.illumina.parser
Represents one set of cycles in an ReadStructure (e.g.
ReadDescriptor(int, ReadType) - Constructor for class picard.illumina.parser.ReadDescriptor
 
ReadEnds - Class in picard.sam.markduplicates.util
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
ReadEnds() - Constructor for class picard.sam.markduplicates.util.ReadEnds
 
ReadEndsForMarkDuplicates - Class in picard.sam.markduplicates.util
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
ReadEndsForMarkDuplicates() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
ReadEndsForMarkDuplicatesCodec - Class in picard.sam.markduplicates.util
Coded for ReadEnds that just outputs the primitive fields and reads them back.
ReadEndsForMarkDuplicatesCodec() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
ReadEndsForMarkDuplicatesMap - Interface in picard.sam.markduplicates.util
Interface for storing and retrieving ReadEnds objects.
ReadEndsForMateCigar - Class in picard.sam.markduplicates.util
A class to store individual records for MarkDuplicatesWithMateCigar.
ReadEndsForMateCigar(SAMFileHeader, SamRecordWithOrdinal, OpticalDuplicateFinder, short) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMateCigar
Builds a read ends object that represents a single read.
ReadEndsForMateCigar(ReadEndsForMateCigar, SamRecordWithOrdinal) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMateCigar
Creates a shallow copy from the "other"
readGroup - Variable in class picard.sam.markduplicates.util.ReadEnds
 
readLaneTiles(File, ReadStructure) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.
readLengths - Variable in class picard.illumina.parser.ReadStructure
 
ReadNameEncoder - Interface in picard.fastq
 
ReadNameParsingUtils - Class in picard.sam.util
Common functions for quickly parsing strings.
ReadNameParsingUtils() - Constructor for class picard.sam.util.ReadNameParsingUtils
 
readNameRegex - Variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
readNextLine() - Method in class picard.util.AbstractInputParser
 
readNextLine() - Method in class picard.util.BasicInputParser
Workhorse method that reads the next line from the underlying reader
READS - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
The total number of reads matching the barcode.
READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The total number of reads examined
READS_ALIGNED - Variable in class picard.analysis.RrbsSummaryMetrics
Number of mapped reads processed
READS_ALIGNED_IN_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of aligned reads whose mate pair was also aligned to the reference.
READS_IGNORED_MISMATCHES - Variable in class picard.analysis.RrbsSummaryMetrics
Number of reads discarded for exceeding the mismatch threshold
READS_IGNORED_SHORT - Variable in class picard.analysis.RrbsSummaryMetrics
Number of reads discarded due to being too short
READS_TO_ALIGN - Variable in class picard.fastq.BamToBfq
 
READS_WITH_NO_CPG - Variable in class picard.analysis.RrbsSummaryMetrics
Number of reads discarded for having no CpG sites
ReadStructure - Class in picard.illumina.parser
Describes the intended logical output structure of clusters of an Illumina run.
ReadStructure(List<ReadDescriptor>) - Constructor for class picard.illumina.parser.ReadStructure
Copies collection into descriptors (making descriptors unmodifiable) and then calculates relevant statistics about descriptors.
ReadStructure(String) - Constructor for class picard.illumina.parser.ReadStructure
Converts readStructureString into a List and calls the primary constructor using this List as it's argument.
ReadStructure.Substructure - Class in picard.illumina.parser
Represents a subset of ReadDescriptors in the containing ReadStructure, they ARE NOT necessarily contiguous in the containing ReadStrucure but they ARE in the order they appear in the containing ReadStructure
ReadStructure.Substructure(List<Integer>, List<Range>) - Constructor for class picard.illumina.parser.ReadStructure.Substructure
Indices into the ReadStructure.descriptors for this specific substructure, indices must be in the order they appear in the descriptors list (but the indices do NOT have to be continuous)
ReadType - Enum in picard.illumina.parser
A read type describes a stretch of cycles in an ReadStructure (e.g.
RECORDS_ONLY - Variable in class picard.sam.ViewSam
 
REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The (upper-case) original base on the reference strand.
REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The (upper-case) original base on the reference strand.
REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The (upper-case) original base on the reference strand.
REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The (upper-case) original base on the reference strand.
REF_FLAT - Variable in class picard.analysis.CollectRnaSeqMetrics
 
REF_NONOXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The number of reference alleles observed as C in read 1 and G in read 2.
REF_OXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The number of reference alleles observed as G in read 1 and C in read 2.
REF_TOTAL_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The total number of reference alleles observed
REFERENCE - Variable in class picard.analysis.CollectRrbsMetrics
 
REFERENCE - Variable in class picard.sam.CreateSequenceDictionary
 
REFERENCE - Variable in class picard.sam.ReorderSam
 
REFERENCE - Variable in class picard.util.ScatterIntervalsByNs
 
REFERENCE_SEQUENCE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
 
REFERENCE_SEQUENCE - Variable in class picard.analysis.CollectOxoGMetrics
 
REFERENCE_SEQUENCE - Variable in class picard.analysis.CollectWgsMetrics
 
REFERENCE_SEQUENCE - Variable in class picard.cmdline.CommandLineProgram
 
REFERENCE_SEQUENCE - Variable in class picard.reference.ExtractSequences
 
REFERENCE_SEQUENCE - Variable in class picard.sam.MergeBamAlignment
 
REFERENCE_SEQUENCE - Variable in class picard.util.BaitDesigner
 
REFERENCE_SEQUENCE - Variable in class picard.vcf.LiftoverVcf
 
REFERENCE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
referenceFasta - Variable in class picard.sam.AbstractAlignmentMerger
 
RefFlatReader - Class in picard.annotation
Loads gene annotations from a refFlat file into an OverlapDetector.
RefFlatReader.RefFlatColumns - Enum in picard.annotation
 
reflectiveCopy(TargetMetrics, MT, String[], String[]) - Static method in class picard.analysis.directed.TargetMetricsCollector
Since the targeted metrics (HsMetrics, TargetedPcrMetrics,...) share many of the same values as TargetMetrics, this copy will copy all public attributes in targetMetrics to the outputMetrics' attributes of the same name.
REJECT - Variable in class picard.vcf.LiftoverVcf
 
remove() - Method in class picard.illumina.parser.IlluminaDataProvider
 
remove() - Method in class picard.illumina.parser.MultiTileParser
 
remove() - Method in class picard.illumina.parser.PerTileParser
 
remove() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
 
remove() - Method in class picard.illumina.parser.readers.BarcodeFileReader
 
remove() - Method in class picard.illumina.parser.readers.BclReader
 
remove() - Method in class picard.illumina.parser.readers.FilterFileReader
 
remove() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
 
remove() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
remove(int, String) - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
 
remove(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
Removes the end from this set, if present
remove(int, String) - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
Remove element with given key from the map.
remove() - Method in class picard.util.AsyncIterator
 
remove() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
remove() - Method in class picard.vcf.ByIntervalListVariantContextIterator
 
remove() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
 
remove() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
 
REMOVE_ALIGNMENT_INFORMATION - Variable in class picard.sam.RevertSam
 
REMOVE_DUPLICATE_INFORMATION - Variable in class picard.sam.PositionBasedDownsampleSam
 
REMOVE_DUPLICATE_INFORMATION - Variable in class picard.sam.RevertSam
 
REMOVE_DUPLICATES - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
removeIncompleteTrios() - Method in class picard.pedigree.PedFile
Scans through the pedigrees and removes all entries that do not have both paternal and maternal ids set.
removeLocationSet() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
RenameSampleInVcf - Class in picard.vcf
 
RenameSampleInVcf() - Constructor for class picard.vcf.RenameSampleInVcf
 
renderTileMetricsFileFromBasecallingDirectory(File) - Static method in class picard.illumina.parser.TileMetricsUtil
Returns the path to the TileMetrics file given the basecalling directory.
ReorderSam - Class in picard.sam
Reorders a SAM/BAM input file according to the order of contigs in a second reference sequence
ReorderSam() - Constructor for class picard.sam.ReorderSam
 
REPEAT_TOLERANCE - Variable in class picard.util.BaitDesigner
 
replace(ReadEndsForMateCigar, ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
Replaces a given end with the other end.
ReplaceSamHeader - Class in picard.sam
 
ReplaceSamHeader() - Constructor for class picard.sam.ReplaceSamHeader
 
REQUIRE_INDEX - Variable in class picard.vcf.CollectVariantCallingMetrics
 
REQUIRE_INDEX - Variable in class picard.vcf.VcfFormatConverter
 
resetRefSeqFileWalker() - Method in class picard.sam.AbstractAlignmentMerger
 
RESTORE_ORIGINAL_QUALITIES - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
RESTORE_ORIGINAL_QUALITIES - Variable in class picard.sam.RevertSam
 
result() - Method in class picard.vcf.CallingMetricAccumulator
 
result() - Method in interface picard.vcf.processor.VariantProcessor.Accumulator
 
REV_CXT_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context.
REV_CXT_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context.
REV_ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)).
RevertOriginalBaseQualitiesAndAddMateCigar - Class in picard.sam
This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped BAMs.
RevertOriginalBaseQualitiesAndAddMateCigar() - Constructor for class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile - Enum in picard.sam
Used as a return for the canSkipSAMFile function.
RevertSam - Class in picard.sam
Reverts a SAM file by optionally restoring original quality scores and by removing all alignment information.
RevertSam() - Constructor for class picard.sam.RevertSam
 
revertSamRecord(SAMRecord) - Method in class picard.sam.RevertSam
Takes an individual SAMRecord and applies the set of changes/reversions to it that have been requested by program level options.
reviseAndConditionallyLogQuality(byte) - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
Accepts a quality read from a BCL file and (1) returns a 1 if the value was 0 and (2) makes a note of the provided quality if it is low.
RExecutor - Class in picard.util
Util class for executing R scripts.
RExecutor() - Constructor for class picard.util.RExecutor
 
RF - Static variable in class picard.sam.markduplicates.util.ReadEnds
 
RG_TAG - Variable in class picard.sam.SamToFastq
 
RGCN - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGDS - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGDT - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGID - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGLB - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGPG - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGPI - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGPL - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGPM - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGPU - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGSM - Variable in class picard.sam.AddOrReplaceReadGroups
 
RIBOSOMAL_BASES - Variable in class picard.analysis.RnaSeqMetrics
Number of bases in primary aligments that align to ribosomal sequence.
RIBOSOMAL_INTERVALS - Variable in class picard.analysis.CollectRnaSeqMetrics
 
RIGHT_PRIMER - Variable in class picard.util.BaitDesigner
 
RnaSeqMetrics - Class in picard.analysis
Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics program and usually stored in a file with the extension ".rna_metrics".
RnaSeqMetrics() - Constructor for class picard.analysis.RnaSeqMetrics
 
RnaSeqMetricsCollector - Class in picard.analysis.directed
 
RnaSeqMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, Long, OverlapDetector<Gene>, OverlapDetector<Interval>, HashSet<Integer>, int, RnaSeqMetricsCollector.StrandSpecificity, double, boolean) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector
 
RnaSeqMetricsCollector.StrandSpecificity - Enum in picard.analysis.directed
 
round(double, int) - Static method in class picard.util.MathUtil
Round off the value to the specified precision.
RR - Static variable in class picard.sam.markduplicates.util.ReadEnds
 
RrbsCpgDetailMetrics - Class in picard.analysis
Holds information about CpG sites encountered for RRBS processing QC
RrbsCpgDetailMetrics() - Constructor for class picard.analysis.RrbsCpgDetailMetrics
 
RrbsMetricsCollector - Class in picard.analysis
 
RrbsMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, int, int, int, double) - Constructor for class picard.analysis.RrbsMetricsCollector
 
RrbsSummaryMetrics - Class in picard.analysis
Holds summary statistics from RRBS processing QC
RrbsSummaryMetrics() - Constructor for class picard.analysis.RrbsSummaryMetrics
 
RRNA_FRAGMENT_PERCENTAGE - Variable in class picard.analysis.CollectRnaSeqMetrics
 
run() - Method in class picard.Test
 
RUN_BARCODE - Variable in class picard.fastq.BamToBfq
 
RUN_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
RUN_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToSam
 
RUN_DATE - Variable in class picard.sam.FastqToSam
 
RUN_DIRECTORY - Variable in class picard.illumina.CollectIlluminaLaneMetrics
 
RUN_START_DATE - Variable in class picard.illumina.IlluminaBasecallsToSam
 

S

SamAlignmentMerger - Class in picard.sam
Class that takes in a set of alignment information in SAM format and merges it with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
SamAlignmentMerger(File, File, File, SAMProgramRecord, boolean, boolean, boolean, List<File>, int, List<String>, List<String>, Integer, Integer, List<File>, List<File>, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean) - Constructor for class picard.sam.SamAlignmentMerger
Constructor
samFiles - Variable in class picard.sam.CompareSAMs
 
SamFormatConverter - Class in picard.sam
Converts a BAM file to human-readable SAM output or vice versa
SamFormatConverter() - Constructor for class picard.sam.SamFormatConverter
 
SamOrBam - Class in picard.cmdline.programgroups
 
SamOrBam() - Constructor for class picard.cmdline.programgroups.SamOrBam
 
SAMPLE - Variable in class picard.metrics.MultilevelMetrics
The sample to which these metrics apply.
SAMPLE - Variable in class picard.vcf.MakeSitesOnlyVcf
 
SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The name of the sample being assayed.
SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The name of the sample being assayed.
SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The name of the sample being assayed.
SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The name of the sample being assayed.
SAMPLE_ALIAS - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The name of the sample being assayed.
SAMPLE_ALIAS - Variable in class picard.illumina.IlluminaBasecallsToSam
 
SAMPLE_ALIAS - Variable in class picard.sam.RevertSam
 
SAMPLE_ALIAS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
The name of the sample being assayed
SAMPLE_ALIAS_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
SAMPLE_NAME - Variable in class picard.sam.FastqToSam
 
SAMRecordAndReference - Class in picard.metrics
 
SAMRecordAndReference(SAMRecord, ReferenceSequence) - Constructor for class picard.metrics.SAMRecordAndReference
 
SAMRecordAndReferenceMultiLevelCollector<BEAN extends MetricBase,HKEY extends Comparable> - Class in picard.metrics
 
SAMRecordAndReferenceMultiLevelCollector() - Constructor for class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
 
SAMRecordMultiLevelCollector<BEAN extends MetricBase,HKEY extends Comparable> - Class in picard.metrics
Defines a MultilevelPerRecordCollector using the argument type of SAMRecord so that this doesn't have to be redefined for each subclass of MultilevelPerRecordCollector
SAMRecordMultiLevelCollector() - Constructor for class picard.metrics.SAMRecordMultiLevelCollector
 
samRecordWithOrdinal - Variable in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
SamRecordWithOrdinalAndSetDuplicateReadFlag - Class in picard.sam.markduplicates.util
This class sets the duplicate read flag as the result state when examining sets of records.
SamRecordWithOrdinalAndSetDuplicateReadFlag() - Constructor for class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
 
SamRecordWithOrdinalAndSetDuplicateReadFlag(SAMRecord, long) - Constructor for class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
 
SamToFastq - Class in picard.sam

Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger fastq format.

SamToFastq() - Constructor for class picard.sam.SamToFastq
 
SANITIZE - Variable in class picard.sam.RevertSam
 
scanDir(File, String) - Method in class picard.cmdline.ClassFinder
Scans a directory on the filesystem for classes.
scanJar(File, String) - Method in class picard.cmdline.ClassFinder
Scans the entries in a ZIP/JAR file for classes under the parent package.
scatter(IntervalList, int) - Method in class picard.util.IntervalListScatterer
 
scatter(IntervalList, int, boolean) - Method in class picard.util.IntervalListScatterer
 
SCATTER_COUNT - Variable in class picard.util.IntervalListTools
 
ScatterIntervalsByNs - Class in picard.util
A CLP for breaking up a reference into intervals of Ns and ACGTs bases.
ScatterIntervalsByNs() - Constructor for class picard.util.ScatterIntervalsByNs
 
scheme - Variable in class picard.vcf.GenotypeConcordanceScheme
The underlying scheme
score - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
SD_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The standard deviation of clusters per tile.
SD_COVERAGE - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
The standard deviation of coverage of the genome after all filters are applied.
SD_PCT_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The standard deviation in percentage of pf clusters per tile.
SD_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The standard deviation in number of pf clusters per tile.
SECOND_END_FASTQ - Variable in class picard.sam.SamToFastq
 
SECOND_INPUT - Variable in class picard.util.IntervalListTools
 
seek(List<File>, TileIndex, int) - Method in class picard.illumina.parser.readers.BclReader
 
seekToTile(int) - Method in class picard.illumina.parser.IlluminaDataProvider
Jump so that the next record returned will be from the specified tile.
seekToTile(int) - Method in class picard.illumina.parser.MultiTileParser
 
seekToTile(int) - Method in class picard.illumina.parser.PerTileParser
 
segregateReference(ReferenceSequenceFile, int) - Static method in class picard.util.ScatterIntervalsByNs
**************************************************************** Generate an interval list that alternates between Ns and ACGTs * ****************************************************************
seq(double, double, double) - Static method in class picard.util.MathUtil
Mimic's R's seq() function to produce a sequence of equally spaced numbers.
SEQUENCE_DICTIONARY - Variable in class picard.util.BedToIntervalList
 
SEQUENCE_DICTIONARY - Variable in class picard.util.LiftOverIntervalList
 
SEQUENCE_DICTIONARY - Variable in class picard.vcf.CollectVariantCallingMetrics
 
SEQUENCE_DICTIONARY - Variable in class picard.vcf.MergeVcfs
 
SEQUENCE_DICTIONARY - Variable in class picard.vcf.SortVcf
 
SEQUENCE_DICTIONARY - Variable in class picard.vcf.SplitVcfs
 
SEQUENCE_DICTIONARY - Variable in class picard.vcf.UpdateVcfSequenceDictionary
 
SEQUENCE_DICTIONARY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
SEQUENCE_NAME - Variable in class picard.analysis.RrbsCpgDetailMetrics
Sequence the CpG is seen in
SEQUENCE_NAMES - Variable in class picard.analysis.CollectRrbsMetrics
 
SEQUENCING_CENTER - Variable in class picard.illumina.IlluminaBasecallsToSam
 
SEQUENCING_CENTER - Variable in class picard.sam.FastqToSam
 
SequencingArtifactMetrics - Class in picard.analysis.artifacts
 
SequencingArtifactMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics
 
SequencingArtifactMetrics.BaitBiasDetailMetrics - Class in picard.analysis.artifacts
Bait bias artifacts broken down by context.
SequencingArtifactMetrics.BaitBiasDetailMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
 
SequencingArtifactMetrics.BaitBiasSummaryMetrics - Class in picard.analysis.artifacts
Summary analysis of a single bait bias artifact, also known as a reference bias artifact.
SequencingArtifactMetrics.BaitBiasSummaryMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
 
SequencingArtifactMetrics.PreAdapterDetailMetrics - Class in picard.analysis.artifacts
Pre-adapter artifacts broken down by context.
SequencingArtifactMetrics.PreAdapterDetailMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
 
SequencingArtifactMetrics.PreAdapterSummaryMetrics - Class in picard.analysis.artifacts
Summary analysis of a single pre-adapter artifact.
SequencingArtifactMetrics.PreAdapterSummaryMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
 
setApplyEamssFiltering(boolean) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
Sets whether or not EAMSS filtering will be applied if parsing BCL files for bases and quality scores.
setBaitSetName(String) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
Sets the name of the bait set explicitly instead of inferring it from the bait file.
setBases(byte[]) - Method in class picard.illumina.parser.ReadData
 
setClipOverlappingReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
 
setConverter(IlluminaBasecallsConverter.ClusterDataConverter<CLUSTER_OUTPUT_RECORD>) - Method in class picard.illumina.IlluminaBasecallsConverter
Must be called before doTileProcessing.
setDefaultHeaders(List<Header>) - Method in class picard.cmdline.CommandLineProgram
 
setIncludeSecondaryAlignments(boolean) - Method in class picard.sam.AbstractAlignmentMerger
 
setInputStream(InputStream) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
setKeepAlignerProperPairFlags(boolean) - Method in class picard.sam.AbstractAlignmentMerger
If true, keep the aligner's idea of proper pairs rather than letting alignment merger decide.
setLane(int) - Method in class picard.illumina.parser.ClusterData
 
setLibraryId(short) - Method in interface picard.sam.markduplicates.util.OpticalDuplicateFinder.PhysicalLocation
 
setLibraryId(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
setLibraryId(short) - Method in class picard.sam.markduplicates.util.ReadEnds
 
setLocationSet(PhysicalLocationForMateCigarSet) - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
setMatchedBarcode(String) - Method in class picard.illumina.parser.ClusterData
 
setMaxPairErrorRate(double) - Method in class picard.util.AdapterMarker
 
setMaxRecordsInRam(int) - Method in class picard.sam.AbstractAlignmentMerger
Allows the caller to override the maximum records in RAM.
setMaxSingleEndErrorRate(double) - Method in class picard.util.AdapterMarker
 
setMessageStream(PrintStream) - Method in class picard.cmdline.CommandLineParser
This method is only needed when calling one of the public methods that doesn't take a messageStream argument.
setMinPairMatchBases(int) - Method in class picard.util.AdapterMarker
 
setMinSingleEndMatchBases(int) - Method in class picard.util.AdapterMarker
 
setNoise(FourChannelIntensityData) - Method in class picard.illumina.parser.ReadData
 
setNumAdaptersToKeep(int) - Method in class picard.util.AdapterMarker
After seeing the thresholdForSelectingAdapters number of adapters, keep up to this many of the original adapters.
setOrCheckLane(int) - Method in class picard.illumina.parser.ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckPf(boolean) - Method in class picard.illumina.parser.ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckTile(int) - Method in class picard.illumina.parser.ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckX(int) - Method in class picard.illumina.parser.ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckY(int) - Method in class picard.illumina.parser.ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOutputStream(OutputStream) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
setPerTargetOutput(File) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
If set, the metrics collector will output per target coverage information to this file.
setPf(boolean) - Method in class picard.illumina.parser.ClusterData
 
setProgramRecord(SAMProgramRecord) - Method in class picard.sam.AbstractAlignmentMerger
 
setProgramsToRun(List<CollectMultipleMetrics.ProgramInterface>) - Method in class picard.analysis.CollectMultipleMetrics
Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones available via enum.
setQualities(byte[]) - Method in class picard.illumina.parser.ReadData
 
setRawIntensities(FourChannelIntensityData) - Method in class picard.illumina.parser.ReadData
 
setReadGroup(short) - Method in interface picard.sam.markduplicates.util.OpticalDuplicateFinder.PhysicalLocation
 
setReadGroup(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
setReadGroup(short) - Method in class picard.sam.markduplicates.util.ReadEnds
 
setReadType(ReadType) - Method in class picard.illumina.parser.ReadData
 
setResultState(boolean) - Method in class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
 
setSkipBlankLines(boolean) - Method in class picard.util.AbstractInputParser
 
setThresholdForSelectingAdaptersToKeep(int) - Method in class picard.util.AdapterMarker
When this number of adapters have been matched, discard the least-frequently matching ones.
setTile(int) - Method in class picard.illumina.parser.ClusterData
 
setTile(short) - Method in interface picard.sam.markduplicates.util.OpticalDuplicateFinder.PhysicalLocation
 
setTile(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
setTile(short) - Method in class picard.sam.markduplicates.util.ReadEnds
 
setTile(short) - Method in class picard.sam.util.PhysicalLocation
 
setToMarkQueueMinimumDistance(int) - Method in class picard.sam.markduplicates.util.MarkQueue
Sets the minimum genomic distance such that we can be assured that all duplicates have been considered.
setTreatGroupedDelimitersAsOne(boolean) - Method in class picard.util.AbstractInputParser
 
setup(SAMFileHeader, File) - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectAlignmentSummaryMetrics
 
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectBaseDistributionByCycle
 
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectGcBiasMetrics
 
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectInsertSizeMetrics
 
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectRnaSeqMetrics
 
setup(SAMFileHeader, File) - Method in class picard.analysis.MeanQualityByCycle
 
setup(SAMFileHeader, File) - Method in class picard.analysis.QualityScoreDistribution
 
setup(SAMFileHeader, File) - Method in class picard.analysis.SinglePassSamProgram
Should be implemented by subclasses to do one-time initialization work.
setup(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>) - Method in class picard.metrics.MultiLevelCollector
Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor
setupOpticalDuplicateFinder() - Method in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
setValuesFromAlignment(SAMRecord, SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
Sets the values from the alignment record on the unaligned BAM record.
setWordCount(int) - Method in class picard.util.AbstractInputParser
 
setX(int) - Method in class picard.illumina.parser.ClusterData
 
setX(short) - Method in interface picard.sam.markduplicates.util.OpticalDuplicateFinder.PhysicalLocation
 
setX(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
setX(short) - Method in class picard.sam.markduplicates.util.ReadEnds
 
setX(int) - Method in class picard.sam.util.PhysicalLocation
 
setY(int) - Method in class picard.illumina.parser.ClusterData
 
setY(short) - Method in interface picard.sam.markduplicates.util.OpticalDuplicateFinder.PhysicalLocation
 
setY(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
setY(short) - Method in class picard.sam.markduplicates.util.ReadEnds
 
setY(int) - Method in class picard.sam.util.PhysicalLocation
 
Sex - Enum in picard.pedigree
Represents the sex of an individual.
shouldBeInLocations(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.MarkQueue
Returns true if we should track this for optical duplicate detection, false otherwise
SinglePassSamProgram - Class in picard.analysis
Super class that is designed to provide some consistent structure between subclasses that simply iterate once over a coordinate sorted BAM and collect information from the records as the go in order to produce some kind of output.
SinglePassSamProgram() - Constructor for class picard.analysis.SinglePassSamProgram
 
size() - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
 
size() - Method in class picard.sam.markduplicates.util.MarkQueue
The number of records currently in this queue.
size() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
The number of records in this set
size() - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
 
SIZE_OF - Static variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
sizeInRam() - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
 
sizeInRam() - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
 
Skip - Static variable in enum picard.illumina.parser.ReadType
 
skipEmptyFiles - Variable in class picard.illumina.parser.ParameterizedFileUtil
 
skipRecords(int) - Method in class picard.illumina.parser.readers.FilterFileReader
 
skipRecords(int) - Method in class picard.illumina.parser.readers.LocsFileReader
 
skips - Variable in class picard.illumina.parser.ReadStructure
 
SNP_OUTPUT - Variable in class picard.vcf.SplitVcfs
 
SNP_REFERENCE_BIAS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The rate at which reference bases are observed at ref/alt heterozygous SNP sites.
snpCounter - Variable in class picard.vcf.GenotypeConcordance
 
snps - Variable in class picard.util.DbSnpBitSetUtil.DbSnpBitSets
 
SORT - Variable in class picard.util.BedToIntervalList
 
SORT - Variable in class picard.util.IntervalListTools
 
SORT_ORDER - Variable in class picard.sam.AddOrReplaceReadGroups
 
SORT_ORDER - Variable in class picard.sam.FastqToSam
 
SORT_ORDER - Variable in class picard.sam.FilterSamReads
 
SORT_ORDER - Variable in class picard.sam.FixMateInformation
 
SORT_ORDER - Variable in class picard.sam.MergeBamAlignment
 
SORT_ORDER - Variable in class picard.sam.MergeSamFiles
 
SORT_ORDER - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
SORT_ORDER - Variable in class picard.sam.RevertSam
 
SORT_ORDER - Variable in class picard.sam.SortSam
 
SORT_ORDER_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
SORTING_COLLECTION_SIZE_RATIO - Variable in class picard.sam.markduplicates.MarkDuplicates
 
SortSam - Class in picard.sam
 
SortSam() - Constructor for class picard.sam.SortSam
 
SortVcf - Class in picard.vcf
Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate.
SortVcf() - Constructor for class picard.vcf.SortVcf
 
SPECIES - Variable in class picard.sam.CreateSequenceDictionary
 
split(String, String[], String) - Method in class picard.Test
 
SplitSamByLibrary - Class in picard.sam
Command-line program to split a SAM or BAM file into separate files based on library name.
SplitSamByLibrary() - Constructor for class picard.sam.SplitSamByLibrary
 
SplitVcfs - Class in picard.vcf
Splits the input VCF file into two, one for indels and one for SNPs.
SplitVcfs() - Constructor for class picard.vcf.SplitVcfs
 
STANDARD_DEVIATION - Variable in class picard.analysis.InsertSizeMetrics
Standard deviation of insert sizes over the "core" of the distribution.
StandardOptionDefinitions - Class in picard.cmdline
A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) is the standard long Option name, and the value of the constant is the standard shortName.
StandardOptionDefinitions() - Constructor for class picard.cmdline.StandardOptionDefinitions
 
start - Variable in class picard.annotation.Gene.Transcript.Exon
 
start() - Method in class picard.annotation.Gene.Transcript
 
start - Variable in class picard.illumina.parser.Range
 
start(RootDoc) - Static method in class picard.util.MetricsDoclet
Entry point called by the javadoc command line tool.
start() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
 
start() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
Starts the work of the executor, returning immediately.
start() - Method in class picard.vcf.processor.VcfFileSegment
 
stddev(double[], int, int) - Static method in class picard.util.MathUtil
Calculated the standard deviation of an array of doubles.
stddev(double[], int, int, double) - Static method in class picard.util.MathUtil
Calculated the standard deviation of an array of doubles.
stop() - Method in class picard.vcf.processor.VcfFileSegment
 
STOP_AFTER - Variable in class picard.analysis.CollectMultipleMetrics
 
STOP_AFTER - Variable in class picard.analysis.CollectOxoGMetrics
 
STOP_AFTER - Variable in class picard.analysis.CollectWgsMetrics
 
STOP_AFTER - Variable in class picard.analysis.SinglePassSamProgram
 
STOP_AFTER - Variable in class picard.sam.PositionBasedDownsampleSam
 
STRAND_BALANCE - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of PF reads aligned to the positive strand of the genome divided by the number of PF reads aligned to the genome.
STRAND_SPECIFICITY - Variable in class picard.analysis.CollectRnaSeqMetrics
 
STRICT - Variable in class picard.vcf.SplitVcfs
 
STRIP_UNPAIRED_MATE_NUMBER - Variable in class picard.sam.FastqToSam
 
SUBDIVISION_MODE - Variable in class picard.util.IntervalListTools
 
sum(double...) - Method in class picard.util.MathUtil.LogMath
Computes the sum of the provided log values.
sum(double[], double[]) - Static method in class picard.util.MathUtil
calculates the sum of the arrays as a third array.
sum(double[]) - Static method in class picard.util.MathUtil
Returns the sum of the elements in the array.
sum(long[], int, int) - Static method in class picard.util.MathUtil
Returns the sum of the elements in the array starting with start and ending before stop.
SUMMARY - Variable in class picard.metrics.GcBiasMetrics
 
SUMMARY_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
 
SUMMARY_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
 
SUMMARY_OUTPUT - Variable in class picard.analysis.CollectGcBiasMetrics
 
summaryMetricsExtension - Static variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
supportedTypes() - Method in class picard.illumina.parser.MultiTileParser
 
supportedTypes() - Method in class picard.illumina.parser.PosParser
 

T

TabbedInputParser - Class in picard.util
Parser for tab-delimited files
TabbedInputParser(boolean, InputStream...) - Constructor for class picard.util.TabbedInputParser
Constructor
TabbedInputParser(boolean, File...) - Constructor for class picard.util.TabbedInputParser
Constructor
TabbedTextFileWithHeaderParser - Class in picard.util
Parse a tabbed text file in which columns are found by looking at a header line rather than by position.
TabbedTextFileWithHeaderParser(TabbedInputParser) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
 
TabbedTextFileWithHeaderParser(File) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
 
TabbedTextFileWithHeaderParser(File, String[]) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
 
TabbedTextFileWithHeaderParser.Row - Class in picard.util
 
TAIL_LIMIT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
 
TANDEM_READS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
TARGET_INTERVALS - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
TARGET_INTERVALS - Variable in class picard.vcf.CollectVariantCallingMetrics
 
TARGET_TERRITORY - Variable in class picard.analysis.directed.HsMetrics
The unique number of target bases in the experiment where target is usually exons etc.
TARGET_TERRITORY - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of unique bases covered by the intervals of all targets that should be covered
TargetedPcrMetrics - Class in picard.analysis.directed
Metrics class for targeted pcr runs such as TSCA runs
TargetedPcrMetrics() - Constructor for class picard.analysis.directed.TargetedPcrMetrics
 
TargetedPcrMetricsCollector - Class in picard.analysis.directed
Calculates HS metrics for a given SAM or BAM file.
TargetedPcrMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, IntervalList, IntervalList, String) - Constructor for class picard.analysis.directed.TargetedPcrMetricsCollector
 
TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics> - Class in picard.analysis.directed
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
TargetMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, IntervalList, IntervalList, String) - Constructor for class picard.analysis.directed.TargetMetricsCollector
 
TargetMetricsCollector.Coverage - Class in picard.analysis.directed
A simple class that is used to store the coverage information about an interval.
TargetMetricsCollector.Coverage(Interval, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector.Coverage
Constructs a new coverage object for the provided mapping with the desired padding either side.
TargetMetricsCollector.PerUnitTargetMetricCollector - Class in picard.analysis.directed
Collect the Target Metrics for one unit of "accumulation" (i.e.
TargetMetricsCollector.PerUnitTargetMetricCollector(String, Set<Interval>, String, String, String, long, long, long, Map<Interval, Double>) - Constructor for class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
Constructor that parses the squashed reference to genome reference file and stores the information in a map for later use.
TARGETS - Variable in class picard.util.BaitDesigner
 
Template - Static variable in enum picard.illumina.parser.ReadType
 
templates - Variable in class picard.illumina.parser.ReadStructure
 
Test - Class in picard
 
Test() - Constructor for class picard.Test
 
testDoWork() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
Silly method that is necessary to give unit test access to call doWork()
Testing - Class in picard.cmdline.programgroups
 
Testing() - Constructor for class picard.cmdline.programgroups.Testing
 
TestNGUtil - Class in picard.util
Small class implementing some utility functions that are useful for test and interfacing with the TestNG framework.
TestNGUtil() - Constructor for class picard.util.TestNGUtil
 
TestNGUtil.SingleTestUnitTest<TestClazz extends TestNGUtil.TestNGParameterizable> - Class in picard.util
 
TestNGUtil.SingleTestUnitTest() - Constructor for class picard.util.TestNGUtil.SingleTestUnitTest
 
TestNGUtil.TestNGParameterizable - Class in picard.util
Interface for exposing an implementation for converting an object into a Object[] appropriate for positional parameter-passing as performed by TestNG.
TestNGUtil.TestNGParameterizable() - Constructor for class picard.util.TestNGUtil.TestNGParameterizable
 
THREAD_COUNT - Variable in class picard.vcf.CollectVariantCallingMetrics
 
THREE_PRIME_ADAPTER - Variable in class picard.illumina.MarkIlluminaAdapters
 
tile - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
The tile, which is determined from the file name
Tile - Class in picard.illumina.parser
Represents a tile from TileMetricsOut.bin.
Tile(int, int, float, float, TilePhasingValue...) - Constructor for class picard.illumina.parser.Tile
 
TILE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
 
TILE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The Tile that is described by this metric.
tile - Variable in class picard.sam.markduplicates.util.ReadEnds
 
TILE_LIMIT - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
TILE_LIMIT - Variable in class picard.illumina.IlluminaBasecallsToSam
 
TILE_METRICS_OUT_FILE_NAME - Static variable in class picard.illumina.parser.TileMetricsUtil
The expected name of the tile metrics output file.
TILE_NUMBER_COMPARATOR - Static variable in class picard.illumina.IlluminaBasecallsConverter
A comparator for tile numbers, which are not necessarily ordered by the number's value.
TILE_NUMBERS - Variable in class picard.illumina.CheckIlluminaDirectory
 
tileIndex - Variable in class picard.illumina.parser.MultiTileFileUtil
 
TileIndex - Class in picard.illumina.parser
Load a file containing 8-byte records like this: tile number: 4-byte int number of clusters in tile: 4-byte int Number of records to read is determined by reaching EOF.
TileIndex.TileIndexRecord - Class in picard.illumina.parser
 
tileIsSet() - Method in class picard.illumina.parser.ClusterData
 
tileMetricsOut() - Method in class picard.illumina.parser.IlluminaFileUtil
 
TileMetricsOutReader - Class in picard.illumina.parser.readers
Reads a TileMetricsOut file commonly found in the InterOp directory of an Illumina Run Folder.
TileMetricsOutReader(File) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader
Return a TileMetricsOutReader for the specified file
TileMetricsOutReader.IlluminaLaneTileCode - Class in picard.illumina.parser.readers
Helper class which captures the combination of a lane, tile & metric code
TileMetricsOutReader.IlluminaLaneTileCode(int, int, int) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
 
TileMetricsOutReader.IlluminaTileMetrics - Class in picard.illumina.parser.readers
IlluminaPhasingMetrics corresponds to a single record in a TileMetricsOut file
TileMetricsOutReader.IlluminaTileMetrics(ByteBuffer) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
TileMetricsOutReader.IlluminaTileMetrics(int, int, int, float) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
TileMetricsUtil - Class in picard.illumina.parser
Utility for reading the tile data from an Illumina run directory's TileMetricsOut.bin file
TileMetricsUtil() - Constructor for class picard.illumina.parser.TileMetricsUtil
 
TilePhasingValue - Class in picard.illumina.parser
Captures information about a phasing value - Which read it corresponds to, which phasing type and a median value
TilePhasingValue(TileTemplateRead, float, float) - Constructor for class picard.illumina.parser.TilePhasingValue
 
tiles - Variable in class picard.illumina.parser.ParameterizedFileUtil
 
TileTemplateRead - Enum in picard.illumina.parser
Defines the first or second template read for a tile
TMP_DIR - Variable in class picard.cmdline.CommandLineProgram
 
TN_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The TN (true negative) count across all variants
TN_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
TN_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
toClassName(String) - Method in class picard.cmdline.ClassFinder
Convert a filename to a class name by removing '.class' and converting '/'s to '.'s.
toCode() - Method in enum picard.pedigree.Sex
Returns the code used to encode this sex in a ped/fam file.
toObjectArray() - Method in class picard.util.TestNGUtil.TestNGParameterizable
 
toReadStructure() - Method in class picard.illumina.parser.ReadStructure.Substructure
Create a ReadStructure from this substructure composed of only the descriptors contained in this substructure, Any ReadDescriptors not in this substructure are treated as if they don't exist (e.g.
toString() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
 
toString() - Method in class picard.illumina.IlluminaBasecallingMetrics
 
toString() - Method in class picard.illumina.parser.ClusterData
 
toString() - Method in class picard.illumina.parser.Range
 
toString() - Method in class picard.illumina.parser.ReadDescriptor
 
toString() - Method in class picard.illumina.parser.ReadStructure
Converts this object into a String using rules complementary to the single string constructor above.
toString() - Method in class picard.vcf.processor.VcfFileSegment
 
TOTAL_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The total number of basecalls observed at all sites.
TOTAL_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The total number of bases in all reads
TOTAL_BASES - Variable in class picard.illumina.IlluminaBasecallingMetrics
The total number of bases assigned to the index.
TOTAL_CLUSTERS - Variable in class picard.analysis.GcBiasSummaryMetrics
The total number of clusters that were seen in the gc bias calculation.
TOTAL_CLUSTERS - Variable in class picard.illumina.IlluminaBasecallingMetrics
The total number of clusters assigned to the index.
TOTAL_COMPLEX_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of high confidence complex Indel calls that were examined
TOTAL_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of high confidence Indel calls that were examined
TOTAL_MULTIALLELIC_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of high confidence multiallelic SNP calls that were examined
TOTAL_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The total Phred-scaled Q-score for this artifact.
TOTAL_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The total Phred-scaled Q-score for this artifact.
TOTAL_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
The total number of reads including all PF and non-PF reads.
TOTAL_READS - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The total number of reads in the input file
TOTAL_READS - Variable in class picard.analysis.directed.HsMetrics
The total number of reads in the SAM or BAM file examine.
TOTAL_READS - Variable in class picard.analysis.directed.TargetedPcrMetrics
The total number of reads in the SAM or BAM file examine.
TOTAL_READS - Variable in class picard.illumina.IlluminaBasecallingMetrics
The total number of reads assigned to the index.
TOTAL_SITES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The total number of sites that had at least one base covering them.
TOTAL_SITES - Variable in class picard.analysis.RrbsCpgDetailMetrics
Number of times this CpG site was encountered
TOTAL_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of high confidence SNPs calls (i.e.
totalCycles - Variable in class picard.illumina.parser.ReadStructure
 
TP_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The TP (true positive) count across all variants
TP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
TP_FP - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
TP_FP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
TP_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
TP_TN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
trackOpticalDuplicates(List<? extends ReadEnds>, OpticalDuplicateFinder, LibraryIdGenerator) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
Looks through the set of reads and identifies how many of the duplicates are in fact optical duplicates, and stores the data in the instance level histogram.
transcriptionEnd - Variable in class picard.annotation.Gene.Transcript
 
transcriptionStart - Variable in class picard.annotation.Gene.Transcript
 
TRUNCATE_NAMES_AT_WHITESPACE - Variable in class picard.sam.CreateSequenceDictionary
 
TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE - Variable in class picard.reference.NormalizeFasta
 
TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordance
 
TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The name of the 'truth' sample
TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The name of the 'truth' sample
TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The name of the 'truth' sample
TRUTH_STATE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The state of the 'truth' sample (i.e.
TRUTH_VCF - Variable in class picard.vcf.GenotypeConcordance
 
type - Variable in class picard.illumina.parser.ReadDescriptor
 
TYPE_NAME - Variable in class picard.illumina.IlluminaPhasingMetrics
 

U

uByteToInt(byte) - Static method in class picard.util.UnsignedTypeUtil
Convert an unsigned byte to a signed int
uByteToShort(byte) - Static method in class picard.util.UnsignedTypeUtil
Convert an unsigned byte to a signed short
uIntToLong(int) - Static method in class picard.util.UnsignedTypeUtil
Convert an unsigned int to a long
UNIQUE - Variable in class picard.util.BedToIntervalList
 
UNIQUE - Variable in class picard.util.IntervalListTools
 
UNKNOWN - Static variable in class picard.metrics.MultiLevelCollector
 
UNKNOWN_SEX - Static variable in class picard.pedigree.PedFile
 
UNMAPPED_BAM - Variable in class picard.sam.MergeBamAlignment
 
UNMAPPED_READS - Variable in class picard.sam.DuplicationMetrics
The total number of unmapped reads examined.
UNPAIRED_FASTQ - Variable in class picard.sam.SamToFastq
 
UNPAIRED_READ_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
The number of fragments that were marked as duplicates.
UNPAIRED_READS_EXAMINED - Variable in class picard.sam.DuplicationMetrics
The number of mapped reads examined which did not have a mapped mate pair, either because the read is unpaired, or the read is paired to an unmapped mate.
unsafeNextInfo() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
Returns the next position info.
unsafeNextInfo() - Method in class picard.illumina.parser.readers.ClocsFileReader
Grab the next set of offset values, decompress them.
unsafeNextInfo() - Method in class picard.illumina.parser.readers.LocsFileReader
 
unsafeNextInfo() - Method in class picard.illumina.parser.readers.PosFileReader
Read a line of text and parse it into two float values, create a PositionInfo and return it
UnsignedTypeUtil - Class in picard.util
A utility class for dealing with unsigned types.
UnsignedTypeUtil() - Constructor for class picard.util.UnsignedTypeUtil
 
updateCigarForTrimmedOrClippedBases(SAMRecord, SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
 
updateDerivedValuesInPlace() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
 
updateDerivedValuesInPlace() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
 
UpdateVcfSequenceDictionary - Class in picard.vcf
Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
UpdateVcfSequenceDictionary() - Constructor for class picard.vcf.UpdateVcfSequenceDictionary
 
URI - Variable in class picard.sam.CreateSequenceDictionary
 
usage(PrintStream, boolean) - Method in class picard.cmdline.CommandLineParser
Print a usage message based on the options object passed to the ctor.
USAGE - Static variable in class picard.illumina.IlluminaBasecallsToSam
 
USAGE - Variable in class picard.sam.ViewSam
 
USE_OQ - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
USE_OQ - Variable in class picard.analysis.CollectOxoGMetrics
 
USE_ORIGINAL_QUALITIES - Variable in class picard.analysis.CollectQualityYieldMetrics
 
USE_ORIGINAL_QUALITIES_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
USE_SEQUENTIAL_FASTQS - Variable in class picard.sam.FastqToSam
 
USE_THREADING - Variable in class picard.sam.MergeSamFiles
 
USE_VCF_INDEX - Variable in class picard.vcf.GenotypeConcordance
 
usesNoRefReads() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
usesNoRefReads() - Method in class picard.analysis.CollectInsertSizeMetrics
 
usesNoRefReads() - Method in class picard.analysis.SinglePassSamProgram
Can be overriden and set to false if the section of unmapped reads at the end of the file isn't needed.
uShortToInt(short) - Static method in class picard.util.UnsignedTypeUtil
Convert an unsigned short to an Int
UTR_BASES - Variable in class picard.analysis.RnaSeqMetrics
Number of bases in primary aligments that align to a UTR base for some gene, and not a coding base.

V

VALIDATE_INDEX - Variable in class picard.sam.ValidateSamFile
 
validateCountsAgainstScheme(GenotypeConcordanceScheme) - Method in class picard.vcf.GenotypeConcordanceCounts
Validates that there are no counts for NA states in the underlying scheme
ValidateSamFile - Class in picard.sam
Command line program wrapping SamFileValidator.
ValidateSamFile() - Constructor for class picard.sam.ValidateSamFile
 
ValidateSamFile.Mode - Enum in picard.sam
 
validateScheme() - Method in class picard.vcf.GenotypeConcordanceScheme
Check that all cells in the scheme exist.
VALIDATION_STRINGENCY - Variable in class picard.cmdline.CommandLineProgram
 
valueOf(String) - Static method in enum picard.analysis.AlignmentSummaryMetrics.Category
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.CollectMultipleMetrics.Program
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.MetricAccumulationLevel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.annotation.LocusFunction
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.annotation.RefFlatReader.RefFlatColumns
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.IlluminaDataType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.IlluminaMetricsCode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.IntensityChannel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.ReadType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.TileTemplateRead
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.pedigree.Sex
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.ValidateSamFile.Mode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.ViewSam.AlignmentStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.ViewSam.PfStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.BaitDesigner.DesignStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.IntervalListScatterer.Mode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.IntervalListTools.Action
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.VariantType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStateCodes
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
Returns the enum constant of this type with the specified name.
values() - Static method in enum picard.analysis.AlignmentSummaryMetrics.Category
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.CollectMultipleMetrics.Program
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.MetricAccumulationLevel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.annotation.LocusFunction
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.annotation.RefFlatReader.RefFlatColumns
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.IlluminaDataType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.IlluminaMetricsCode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.IntensityChannel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.ReadType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.TileTemplateRead
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.pedigree.Sex
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.ValidateSamFile.Mode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.ViewSam.AlignmentStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.ViewSam.PfStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.BaitDesigner.DesignStrategy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.IntervalListScatterer.Mode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.IntervalListTools.Action
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.VariantType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.vcf.GenotypeConcordanceStateCodes
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
Returns an array containing the constants of this enum type, in the order they are declared.
VAR_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP))
VAR_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN))
VAR_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN))
VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The type of the event (i.e.
VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The type of the event (i.e.
VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The type of the event (i.e.
VariantAccumulatorExecutor<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,RESULT> - Interface in picard.vcf.processor
Describes the functionality for an executor that manages the delegation of work to VariantProcessor.Accumulators.
VariantAccumulatorExecutor.MultiThreadedChunkBased<A extends VariantProcessor.Accumulator<R>,R> - Class in picard.vcf.processor
A VariantAccumulatorExecutor that breaks down work into chunks described by the provided VariantIteratorProducer and spreads them over the indicated number of threads.
VariantAccumulatorExecutor.MultiThreadedChunkBased(int, VariantIteratorProducer, VariantProcessor.AccumulatorGenerator<A, R>) - Constructor for class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
 
VariantFilter - Interface in picard.vcf.filter
Interface for classes that can generate filters for VariantContexts.
VariantIteratorProducer - Class in picard.vcf.processor
A mechanism for iterating over CloseableIterator of VariantContexts in in some fashion, given VCF files and optionally an interval list.
VariantIteratorProducer() - Constructor for class picard.vcf.processor.VariantIteratorProducer
 
VariantProcessor<RESULT,ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>> - Class in picard.vcf.processor
Describes an object that processes variants and produces a result.
VariantProcessor.Accumulator<RESULT> - Interface in picard.vcf.processor
Handles VariantContexts, and accumulates their data in some fashion internally.
VariantProcessor.AccumulatorGenerator<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,RESULT> - Interface in picard.vcf.processor
Generates instances of VariantProcessor.Accumulators.
VariantProcessor.Builder<A extends VariantProcessor.Accumulator<R>,R> - Class in picard.vcf.processor
Simple builder of VariantProcessors.
VariantProcessor.ResultMerger<RESULT> - Interface in picard.vcf.processor
Takes a collection of results produced by VariantProcessor.Accumulator.result() and merges them into a single RESULT.
VariantType - Enum in picard.util
Enum to hold the possible types of dbSnps.
vcf() - Method in class picard.vcf.processor.VcfFileSegment
 
VcfFileSegment - Class in picard.vcf.processor
Describes a segment of a particular VCF file.
VcfFileSegment() - Constructor for class picard.vcf.processor.VcfFileSegment
 
VcfFileSegmentGenerator - Class in picard.vcf.processor
Describes a mechanism for producing VcfFileSegments from a VCF file.
VcfFileSegmentGenerator() - Constructor for class picard.vcf.processor.VcfFileSegmentGenerator
 
VcfFormatConverter - Class in picard.vcf
Converts an ASCII VCF file to a binary BCF or vice versa.
VcfFormatConverter() - Constructor for class picard.vcf.VcfFormatConverter
 
VcfOrBcf - Class in picard.cmdline.programgroups
 
VcfOrBcf() - Constructor for class picard.cmdline.programgroups.VcfOrBcf
 
VcfToIntervalList - Class in picard.vcf
Creates an interval list from a VCF
VcfToIntervalList() - Constructor for class picard.vcf.VcfToIntervalList
 
VERBOSITY - Variable in class picard.cmdline.CommandLineProgram
 
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclFileUtil
 
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileFileUtil
expectedCycles are not checked in this implementation.
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.ParameterizedFileUtil
Given the expected tiles/expected cycles for this file type, return a list of error messages describing any missing/or malformed files
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileFileUtil
 
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
 
verify(List<Integer>) - Method in class picard.illumina.parser.TileIndex
 
verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileParser
 
verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileParser
 
version - Variable in class picard.illumina.parser.readers.FilterFileReader
Version number found in the FilterFile, this should equal 3
ViewSam - Class in picard.sam
Very simple command that just reads a SAM or BAM file and writes out the header and each records to standard out.
ViewSam() - Constructor for class picard.sam.ViewSam
 
ViewSam.AlignmentStatus - Enum in picard.sam
 
ViewSam.PfStatus - Enum in picard.sam
 

W

WIDTH_OF_10_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 10% of all read pairs.
WIDTH_OF_20_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 20% of all read pairs.
WIDTH_OF_30_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 30% of all read pairs.
WIDTH_OF_40_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 40% of all read pairs.
WIDTH_OF_50_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 50% of all read pairs.
WIDTH_OF_60_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 60% of all read pairs.
WIDTH_OF_70_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 70% of all read pairs.
WIDTH_OF_80_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 80% of all read pairs.
WIDTH_OF_90_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 90% of all read pairs.
WIDTH_OF_99_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 100% of all read pairs.
WINDOW_SIZE - Variable in class picard.analysis.CollectGcBiasMetrics
 
WINDOW_SIZE - Variable in class picard.analysis.GcBiasSummaryMetrics
The window size on the genome used to calculate the GC of the sequence.
WINDOWS - Variable in class picard.analysis.GcBiasDetailMetrics
The number of windows on the reference genome that have this G+C content.
withInput(File...) - Method in class picard.vcf.processor.VariantProcessor.Builder
 
WORST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
WORST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
WORST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The Q-score for the worst context.
WORST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The Q-score for the worst context.
WORST_POST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
WORST_POST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
WORST_POST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The Q-score for the worst post-context.
WORST_POST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The Q-score for the worst post-context.
WORST_PRE_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
WORST_PRE_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
WORST_PRE_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The Q-score for the worst pre-context.
WORST_PRE_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The Q-score for the worst pre-context.
write(OUTPUT_RECORD) - Method in interface picard.illumina.IlluminaBasecallsConverter.ConvertedClusterDataWriter
 
write(File) - Method in class picard.pedigree.PedFile
Writes a set of pedigrees out to disk.
write(byte[], int, int) - Method in class picard.util.CircularByteBuffer
Write bytes into the buffer from the supplied array.
WRITE_READS_FILES - Variable in class picard.sam.FilterSamReads
 
writeAlignment(SAMRecord) - Method in class picard.sam.FixMateInformation
 
writeBfqFiles() - Method in class picard.fastq.BamToBfqWriter
Writes the binary fastq file(s) to the output directory
writeLaneMetrics(Map<Integer, Collection<Tile>>, File, String, MetricsFile<MetricBase, Comparable<?>>) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
 
writePhasingMetrics(Map<Integer, Collection<Tile>>, File, String, MetricsFile<MetricBase, Comparable<?>>) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
 

X

X - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
 
x - Variable in class picard.sam.markduplicates.util.ReadEnds
 
xIsSet() - Method in class picard.illumina.parser.ClusterData
 
xPos - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
The x-position as it occurs in the file being read
xQseqCoord - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
The QSeq style x-coordinat, an integer = Math.round(xPos*10 + 1000)

Y

Y - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
 
y - Variable in class picard.sam.markduplicates.util.ReadEnds
 
yIsSet() - Method in class picard.illumina.parser.ClusterData
 
yPos - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
The y-position as it occurs in the file being read
yQseqCoord - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
The QSeq style y-coordinates, an integer = Math.round(yPos*10 + 1000)

Z

ZERO_CVG_TARGETS_PCT - Variable in class picard.analysis.directed.HsMetrics
The number of targets that did not reach coverage=2 over any base.
ZERO_CVG_TARGETS_PCT - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of targets that did not reach coverage=2 over any base.
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