public class CollectWgsMetrics extends CommandLineProgram
Modifier and Type | Class and Description |
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static class |
CollectWgsMetrics.WgsMetrics
Metrics for evaluating the performance of whole genome sequencing experiments.
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Modifier and Type | Field and Description |
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boolean |
COUNT_UNPAIRED |
int |
COVERAGE_CAP |
boolean |
INCLUDE_BQ_HISTOGRAM |
File |
INPUT |
int |
LOCUS_ACCUMULATION_CAP |
int |
MINIMUM_BASE_QUALITY |
int |
MINIMUM_MAPPING_QUALITY |
File |
OUTPUT |
File |
REFERENCE_SEQUENCE |
int |
SAMPLE_SIZE |
long |
STOP_AFTER |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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CollectWgsMetrics() |
Modifier and Type | Method and Description |
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protected int |
doWork()
Do the work after command line has been parsed.
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protected CollectWgsMetrics.WgsMetrics |
generateWgsMetrics() |
protected long |
getBasesExcludedBy(CountingFilter filter) |
protected SamLocusIterator |
getLocusIterator(SamReader in) |
static void |
main(String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="R", doc="The reference sequence fasta aligned to.") public File REFERENCE_SEQUENCE
@Option(shortName="MQ", doc="Minimum mapping quality for a read to contribute coverage.", overridable=true) public int MINIMUM_MAPPING_QUALITY
@Option(shortName="Q", doc="Minimum base quality for a base to contribute coverage.", overridable=true) public int MINIMUM_BASE_QUALITY
@Option(shortName="CAP", doc="Treat positions with coverage exceeding this value as if they had coverage at this value (but calculate the difference for PCT_EXC_CAPPED).", overridable=true) public int COVERAGE_CAP
@Option(doc="At positions with coverage exceeding this value, completely ignore reads that accumulate beyond this value (so that they will not be considered for PCT_EXC_CAPPED). Used to keep memory consumption in check, but could create bias if set too low", overridable=true) public int LOCUS_ACCUMULATION_CAP
@Option(doc="For debugging purposes, stop after processing this many genomic bases.") public long STOP_AFTER
@Option(doc="Determines whether to include the base quality histogram in the metrics file.") public boolean INCLUDE_BQ_HISTOGRAM
@Option(doc="If true, count unpaired reads, and paired reads with one end unmapped") public boolean COUNT_UNPAIRED
public static void main(String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
protected CollectWgsMetrics.WgsMetrics generateWgsMetrics()
protected long getBasesExcludedBy(CountingFilter filter)
protected SamLocusIterator getLocusIterator(SamReader in)