# Serialized Form

- ## Package picard

  - ### Class picard.PicardException extends RuntimeException implements Serializable

- ## Package picard.annotation

  - ### Class picard.annotation.AnnotationException extends PicardException implements Serializable

- ## Package picard.fingerprint

  - ### Class picard.fingerprint.Fingerprint extends TreeMap<HaplotypeBlock,​HaplotypeProbabilities> implements Serializable

    - ### Serialized Fields

      - #### info

            String info

      - #### sample

            String sample

      - #### source

            Path source

  - ### Class picard.fingerprint.FingerprintUtils.VariantContextSet extends TreeSet<htsjdk.variant.variantcontext.VariantContext> implements Serializable

- ## Package picard.pedigree

  - ### Class picard.pedigree.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 extends ReadNameParser implements Serializable

    - ### Serialized Fields

      - #### bigDuplicateSetSize

            int bigDuplicateSetSize

      - #### maxDuplicateSetSize

            long maxDuplicateSetSize

      - #### opticalDuplicatePixelDistance

            int opticalDuplicatePixelDistance

  - ### Class picard.sam.markduplicates.util.PhysicalLocationForMateCigar extends PhysicalLocationShort implements Serializable

    - ### Serialized Fields

      - #### libraryId

            short libraryId

      - #### readGroup

            short readGroup

  - ### Class picard.sam.markduplicates.util.ReadEnds extends PhysicalLocationShort 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 extends ReadEnds implements Serializable

    - ### Serialized Fields

      - #### duplicateSetSize

            int duplicateSetSize

      - #### read1IndexInFile

            long read1IndexInFile

      - #### read2IndexInFile

            long read2IndexInFile

      - #### score

            short score

  - ### Class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes extends ReadEndsForMarkDuplicates implements Serializable

    - ### Serialized Fields

      - #### barcode

            int barcode

      - #### readOneBarcode

            int readOneBarcode

      - #### readTwoBarcode

            int readTwoBarcode

  - ### Class picard.sam.markduplicates.util.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 extends Object implements Serializable

    - ### Serialized Fields

      - #### tile

            short tile

      - #### x

            int x

      - #### y

            int y

  - ### Class picard.sam.util.PhysicalLocationShort extends PhysicalLocationInt implements Serializable

  - ### Class picard.sam.util.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 extends htsjdk.samtools.util.CollectionUtil.DefaultingMap<String,​Collection<htsjdk.variant.variantcontext.VariantContext>> implements Serializable