Class CountingFilter

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