Package picard.filter

Class CountingFilter

  • All Implemented Interfaces:
    htsjdk.samtools.filter.SamRecordFilter
    Direct Known Subclasses:
    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 Detail

      • CountingFilter

        public CountingFilter()
    • Method Detail

      • 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