# Serialized Form

## Package picard

### Exception Class picard.PicardException

class PicardException extends RuntimeException implements Serializable

## Package picard.annotation

### Exception Class picard.annotation.AnnotationException

class AnnotationException extends PicardException implements Serializable

## Package picard.fingerprint

### Class picard.fingerprint.Fingerprint

class Fingerprint extends TreeMap<HaplotypeBlock, HaplotypeProbabilities> implements Serializable

#### Serialized Fields

##### info

    String info

##### sample

    String sample

##### source

    Path source

### Class picard.fingerprint.FingerprintUtils.VariantContextSet

class VariantContextSet extends TreeSet<htsjdk.variant.variantcontext.VariantContext> implements Serializable

## Package picard.flow

### Class picard.flow.FlowBasedArgumentCollection

class FlowBasedArgumentCollection extends Object implements Serializable

serialVersionUID:
  0L

#### Serialized Fields

##### fillingValue

    double fillingValue

##### ignoreT0Tag

    boolean ignoreT0Tag

## Package picard.nio

### Class picard.nio.PicardHtsPath

class PicardHtsPath extends htsjdk.io.HtsPath implements Serializable

## Package picard.pedigree

### Class picard.pedigree.PedFile

class PedFile extends TreeMap<String, PedFile.PedTrio> implements Serializable

#### Serialized Fields

##### delimiterPattern

    Pattern delimiterPattern

##### delimiterString

    String delimiterString

## Package picard.sam.markduplicates.util

### Class picard.sam.markduplicates.util.OpticalDuplicateFinder

class OpticalDuplicateFinder extends ReadNameParser implements Serializable

#### Serialized Fields

##### bigDuplicateSetSize

    int bigDuplicateSetSize

##### maxDuplicateSetSize

    long maxDuplicateSetSize

##### opticalDuplicatePixelDistance

    int opticalDuplicatePixelDistance

### Class picard.sam.markduplicates.util.PhysicalLocationForMateCigar

class PhysicalLocationForMateCigar extends PhysicalLocationInt implements Serializable

#### Serialized Fields

##### libraryId

    short libraryId

##### readGroup

    short readGroup

### Class picard.sam.markduplicates.util.ReadEnds

class ReadEnds extends PhysicalLocationInt implements Serializable

#### Serialized Fields

##### libraryId

    short libraryId

##### orientation

    byte orientation

##### orientationForOpticalDuplicates

    byte orientationForOpticalDuplicates

For optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate

##### read1Coordinate

    int read1Coordinate

##### read1ReferenceIndex

    int read1ReferenceIndex

##### read2Coordinate

    int read2Coordinate

##### read2ReferenceIndex

    int read2ReferenceIndex

##### readGroup

    short readGroup

### Class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates

class ReadEndsForMarkDuplicates extends ReadEnds implements Serializable

#### Serialized Fields

##### duplicateSetSize

    int duplicateSetSize

##### read1IndexInFile

    long read1IndexInFile

##### read2IndexInFile

    long read2IndexInFile

##### score

    short score

### Class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes

class ReadEndsForMarkDuplicatesWithBarcodes extends ReadEndsForMarkDuplicates implements Serializable

#### Serialized Fields

##### barcode

    int barcode

##### readOneBarcode

    int readOneBarcode

##### readTwoBarcode

    int readTwoBarcode

### Class picard.sam.markduplicates.util.ReadEndsForMateCigar

class ReadEndsForMateCigar extends ReadEnds implements Serializable

#### Serialized Fields

##### hasUnmapped

    byte hasUnmapped

##### 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

## Package picard.sam.util

### Class picard.sam.util.PhysicalLocationInt

class PhysicalLocationInt extends Object implements Serializable

#### Serialized Fields

##### tile

    short tile

##### x

    int x

##### y

    int y

### Class picard.sam.util.PhysicalLocationShort

class PhysicalLocationShort extends PhysicalLocationInt implements Serializable

### Class picard.sam.util.ReadNameParser

class ReadNameParser extends Object implements Serializable

#### Serialized Fields

##### physicalLocationStored

    PhysicalLocation physicalLocationStored

##### readNamePattern

    Pattern readNamePattern

##### readNameRegex

    String readNameRegex

##### readNameStored

    String readNameStored

##### tmpLocationFields

    int[] tmpLocationFields

##### useOptimizedDefaultParsing

    boolean useOptimizedDefaultParsing

##### warnedAboutRegexNotMatching

    boolean warnedAboutRegexNotMatching

## Package picard.vcf.MendelianViolations

### Class picard.vcf.MendelianViolations.MendelianViolationsByFamily

class MendelianViolationsByFamily extends htsjdk.samtools.util.CollectionUtil.DefaultingMap<String, Collection<htsjdk.variant.variantcontext.VariantContext>> implements Serializable