Package picard.filter

Class CountingFilter

java.lang.Object
picard.filter.CountingFilter
All Implemented Interfaces:
htsjdk.samtools.filter.SamRecordFilter
Direct Known Subclasses:
CountingAdapterFilter, CountingDuplicateFilter, CountingMapQFilter, CountingPairedFilter

public abstract class CountingFilter extends Object implements htsjdk.samtools.filter.SamRecordFilter
A SamRecordFilter that counts the number of bases in the reads which it filters out. Abstract and designed to be sub-classed to implement the desired filter. The filterOut method will count the number of records and bases that would be filtered out using the result of the reallyFilterOut method.
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    final boolean
    filterOut(htsjdk.samtools.SAMRecord record)
     
    boolean
    filterOut(htsjdk.samtools.SAMRecord first, htsjdk.samtools.SAMRecord second)
     
    long
    Gets the number of bases that have been filtered out thus far.
    long
    Gets the number of records that have been filtered out thus far.
    abstract boolean
    reallyFilterOut(htsjdk.samtools.SAMRecord record)
    Return true if we are to filter this record out, false otherwise.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Constructor Details

    • CountingFilter

      public CountingFilter()
  • Method Details

    • getFilteredRecords

      public long getFilteredRecords()
      Gets the number of records that have been filtered out thus far.
    • getFilteredBases

      public long getFilteredBases()
      Gets the number of bases that have been filtered out thus far.
    • filterOut

      public final boolean filterOut(htsjdk.samtools.SAMRecord record)
      Specified by:
      filterOut in interface htsjdk.samtools.filter.SamRecordFilter
    • reallyFilterOut

      public abstract boolean reallyFilterOut(htsjdk.samtools.SAMRecord record)
      Return true if we are to filter this record out, false otherwise.
    • filterOut

      public boolean filterOut(htsjdk.samtools.SAMRecord first, htsjdk.samtools.SAMRecord second)
      Specified by:
      filterOut in interface htsjdk.samtools.filter.SamRecordFilter