Serialized Form
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Package picard
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Class picard.PicardException extends RuntimeException implements Serializable
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Package picard.annotation
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Class picard.annotation.AnnotationException extends PicardException implements Serializable
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Package picard.fingerprint
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Class picard.fingerprint.Fingerprint extends TreeMap<HaplotypeBlock,HaplotypeProbabilities> implements Serializable
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Class picard.fingerprint.FingerprintUtils.VariantContextSet extends TreeSet<htsjdk.variant.variantcontext.VariantContext> implements Serializable
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Package picard.nio
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Class picard.nio.PicardHtsPath extends htsjdk.io.HtsPath implements Serializable
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Package picard.pedigree
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Class picard.pedigree.PedFile extends TreeMap<String,PedFile.PedTrio> implements Serializable
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Package picard.sam.markduplicates.util
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Class picard.sam.markduplicates.util.OpticalDuplicateFinder extends ReadNameParser implements Serializable
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Serialized Fields
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bigDuplicateSetSize
int bigDuplicateSetSize
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maxDuplicateSetSize
long maxDuplicateSetSize
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opticalDuplicatePixelDistance
int opticalDuplicatePixelDistance
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Class picard.sam.markduplicates.util.PhysicalLocationForMateCigar extends PhysicalLocationShort implements Serializable
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Serialized Fields
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libraryId
short libraryId
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readGroup
short readGroup
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Class picard.sam.markduplicates.util.ReadEnds extends PhysicalLocationShort implements Serializable
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Serialized Fields
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libraryId
short libraryId
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orientation
byte orientation
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orientationForOpticalDuplicates
byte orientationForOpticalDuplicates
For optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate -
read1Coordinate
int read1Coordinate
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read1ReferenceIndex
int read1ReferenceIndex
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read2Coordinate
int read2Coordinate
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read2ReferenceIndex
int read2ReferenceIndex
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readGroup
short readGroup
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Class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates extends ReadEnds implements Serializable
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Serialized Fields
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duplicateSetSize
int duplicateSetSize
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read1IndexInFile
long read1IndexInFile
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read2IndexInFile
long read2IndexInFile
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score
short score
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Class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes extends ReadEndsForMarkDuplicates implements Serializable
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Serialized Fields
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barcode
int barcode
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readOneBarcode
int readOneBarcode
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readTwoBarcode
int readTwoBarcode
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Class picard.sam.markduplicates.util.ReadEndsForMateCigar extends ReadEnds implements Serializable
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Serialized Fields
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hasUnmapped
byte hasUnmapped
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locationSet
PhysicalLocationForMateCigarSet locationSet
Physical locations used for optical duplicate tracking. This is only stored for paired end reads where both ends are mapped, and when we see the first mate. -
samRecordWithOrdinal
htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal
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Package picard.sam.util
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Class picard.sam.util.PhysicalLocationInt extends Object implements Serializable
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Serialized Fields
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tile
short tile
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x
int x
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y
int y
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Class picard.sam.util.PhysicalLocationShort extends PhysicalLocationInt implements Serializable
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Class picard.sam.util.ReadNameParser extends Object implements Serializable
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Serialized Fields
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physicalLocationStored
PhysicalLocation physicalLocationStored
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readNamePattern
Pattern readNamePattern
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readNameRegex
String readNameRegex
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readNameStored
String readNameStored
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tmpLocationFields
int[] tmpLocationFields
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useOptimizedDefaultParsing
boolean useOptimizedDefaultParsing
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warnedAboutRegexNotMatching
boolean warnedAboutRegexNotMatching
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Package picard.vcf.MendelianViolations
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Class picard.vcf.MendelianViolations.MendelianViolationsByFamily extends htsjdk.samtools.util.CollectionUtil.DefaultingMap<String,Collection<htsjdk.variant.variantcontext.VariantContext>> implements Serializable
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