Uses of Class
picard.PicardException

Packages that use PicardException

Package	Description
picard.annotation
picard.cmdline
picard.sam.markduplicates
picard.vcf

Uses of PicardException in picard.annotation

Subclasses of PicardException in picard.annotation

Modifier and Type	Class and Description
class	AnnotationException Exception thrown when loading gene annotations.

Uses of PicardException in picard.cmdline

Subclasses of PicardException in picard.cmdline

Modifier and Type	Class and Description
class	CommandLineParseException
class	CommandLineParserDefinitionException

Uses of PicardException in picard.sam.markduplicates

Methods in picard.sam.markduplicates that throw PicardException

Modifier and Type	Method and Description
SAMRecord	MarkDuplicatesWithMateCigarIterator.next()

Constructors in picard.sam.markduplicates that throw PicardException

Constructor and Description

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.

Uses of PicardException in picard.vcf

Methods in picard.vcf that throw PicardException

Modifier and Type	Method and Description
void	GenotypeConcordanceScheme.validateScheme() Check that all cells in the scheme exist.