Package | Description |
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picard.annotation | |
picard.cmdline | |
picard.sam.markduplicates | |
picard.vcf |
Modifier and Type | Class and Description |
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class |
AnnotationException
Exception thrown when loading gene annotations.
|
Modifier and Type | Class and Description |
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class |
CommandLineParseException |
class |
CommandLineParserDefinitionException |
Modifier and Type | Method and Description |
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SAMRecord |
MarkDuplicatesWithMateCigarIterator.next() |
Constructor and Description |
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MarkDuplicatesWithMateCigarIterator(SAMFileHeader header,
CloseableIterator<SAMRecord> iterator,
OpticalDuplicateFinder opticalDuplicateFinder,
DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy,
int toMarkQueueMinimumDistance,
boolean removeDuplicates,
boolean skipPairsWithNoMateCigar,
int maxRecordsInRam,
int blockSize,
List<File> tmpDirs)
Initializes the mark duplicates iterator.
|
Modifier and Type | Method and Description |
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void |
GenotypeConcordanceScheme.validateScheme()
Check that all cells in the scheme exist.
|