Package org.broadinstitute.hellbender.tools.dragstr

Class DragstrLocusCase

java.lang.Object
org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase
public final class DragstrLocusCase extends Object
Represents the DRAGstr model fitting relevant stats at a given locus on the genome for the target sample.

  • Constructor Summary

    Constructors
    Constructor
    Description
    DragstrLocusCase(DragstrLocus locus, int total, int nonRef, int minMQ, int nSup)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static DragstrLocusCase
    create(DragstrLocus locus, int depth, int indels, int minMQ, int nSup)
     
    int
    getDepth()
    Returns the total number of qualifying reads that overlap the STR that starts at this locus for the target sample.
    int
    getIndels()
    Returns the total number of indel events on reads that overlap the STR a this locus.
    htsjdk.samtools.util.Locatable
    getLocation(htsjdk.samtools.SAMSequenceDictionary dictionary)
    Returns a locatable for this caze's locus given the sequence dictionary.
    DragstrLocus
    getLocus()
    The target locus.
    int
    getMinMQ()
    The minimum MQ amongst the reads qualifying reads that overlap this position.
    int
    getNSup()
    Number of qualifying reads records that overlap the STR that are supplementary alignments.
    int
    getPeriod()
    The period length of this STR.
    int
    getRepeatLength()
    The repeat lenght in integer repeated units.
    boolean
    qualifies(int minDepth, int samplingMinMQ, int maxSup)
    Tests whether this site can be used for parameter estimation given the limits for relevant stats.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • DragstrLocusCase

      public DragstrLocusCase(DragstrLocus locus, int total, int nonRef, int minMQ, int nSup)

  • Method Details

    • getLocus

      public DragstrLocus getLocus()
      The target locus.
      Returns:
      never null.

    • getPeriod

      public int getPeriod()
      The period length of this STR.
      Returns:
      never null.

    • getRepeatLength

      public int getRepeatLength()
      The repeat lenght in integer repeated units.
      Returns:
      never null.

    • getDepth

      public int getDepth()
      Returns the total number of qualifying reads that overlap the STR that starts at this locus for the target sample.
      Returns:
      0 or greater.

    • getIndels

      public int getIndels()
      Returns the total number of indel events on reads that overlap the STR a this locus.
      Returns:
      0 or greater.

    • getMinMQ

      public int getMinMQ()
      The minimum MQ amongst the reads qualifying reads that overlap this position.
      Returns:
      0 or greater.

    • getNSup

      public int getNSup()
      Number of qualifying reads records that overlap the STR that are supplementary alignments.
      Returns:
      0 or greater.

    • create

      public static DragstrLocusCase create(DragstrLocus locus, int depth, int indels, int minMQ, int nSup)

    • qualifies

      public boolean qualifies(int minDepth, int samplingMinMQ, int maxSup)
      Tests whether this site can be used for parameter estimation given the limits for relevant stats.
      Parameters:
      minDepth - minimum depth to qualify.
      samplingMinMQ - minimum min-MQ.
      maxSup - maximum number of supplementary alignments.
      Returns:
      true iff it qualifies.

    • getLocation

      public htsjdk.samtools.util.Locatable getLocation(htsjdk.samtools.SAMSequenceDictionary dictionary)
      Returns a locatable for this caze's locus given the sequence dictionary.
      Parameters:
      dictionary -
      Returns:
      never null.