Package org.broadinstitute.hellbender.utils.haplotype

Class FlowBasedHaplotype

java.lang.Object
htsjdk.variant.variantcontext.SimpleAllele
org.broadinstitute.hellbender.utils.haplotype.FlowBasedHaplotype
All Implemented Interfaces:
htsjdk.variant.variantcontext.Allele, Serializable, Comparable<htsjdk.variant.variantcontext.Allele>
public class FlowBasedHaplotype extends htsjdk.variant.variantcontext.SimpleAllele
Haplotype that also keeps information on the flow space @see FlowBasedRead Haplotype can't be extended, so this extends Allele
See Also:

  • Field Summary

    Fields inherited from interface htsjdk.variant.variantcontext.Allele

    ALT_A, ALT_C, ALT_G, ALT_N, ALT_T, BREAKEND_EXTENDING_LEFT, BREAKEND_EXTENDING_RIGHT, NO_CALL, NO_CALL_STRING, NON_REF_ALLELE, NON_REF_STRING, REF_A, REF_C, REF_G, REF_N, REF_T, SINGLE_BREAKEND_INDICATOR, SPAN_DEL, SPAN_DEL_STRING, SV_SIMPLE_CNV, SV_SIMPLE_DEL, SV_SIMPLE_DUP, SV_SIMPLE_INS, SV_SIMPLE_INV, SYMBOLIC_ALLELE_END, SYMBOLIC_ALLELE_START, UNSPECIFIED_ALTERNATE_ALLELE, UNSPECIFIED_ALTERNATE_ALLELE_STRING

  • Constructor Summary

    Constructors
    Constructor
    Description
    FlowBasedHaplotype(Haplotype sourceHaplotype, String flowOrder)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    int[]
    findLeftClipping(int baseClipping)
     
    int[]
    findRightClipping(int baseClipping)
     
    String
    getChr()
     
    htsjdk.samtools.Cigar
    getCigar()
     
    int
    getEnd()
     
    byte[]
    getFlowOrderArray()
     
    int[]
    getKey()
     
    int
    getKeyLength()
     
    int
    getStart()
     

    Methods inherited from class htsjdk.variant.variantcontext.SimpleAllele

    basesMatch, basesMatch, basesMatch, compareTo, equals, equals, getBases, getBaseString, getDisplayBases, getDisplayString, hashCode, isBreakpoint, isCalled, isNoCall, isNonRefAllele, isNonReference, isPrefixOf, isReference, isSingleBreakend, isSymbolic, length, toString

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait

  • Constructor Details

    • FlowBasedHaplotype

      public FlowBasedHaplotype(Haplotype sourceHaplotype, String flowOrder)

  • Method Details

    • getKeyLength

      public int getKeyLength()

    • getKey

      public int[] getKey()

    • getStart

      public int getStart()

    • getEnd

      public int getEnd()

    • getChr

      public String getChr()

    • getCigar

      public htsjdk.samtools.Cigar getCigar()

    • findLeftClipping

      public int[] findLeftClipping(int baseClipping)

    • findRightClipping

      public int[] findRightClipping(int baseClipping)

    • getFlowOrderArray

      public byte[] getFlowOrderArray()