Package htsjdk.samtools.filter

Interface SamRecordFilter

All Known Implementing Classes:
AggregateFilter, AlignedFilter, DuplicateReadFilter, FailsVendorReadQualityFilter, HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter, InsertSizeFilter, IntervalFilter, IntervalKeepPairFilter, InvertFilter, JavascriptSamRecordFilter, MappingQualityFilter, NotPrimaryAlignmentFilter, OverclippedReadFilter, ReadNameFilter, SecondaryAlignmentFilter, SecondaryOrSupplementaryFilter, SolexaNoiseFilter, TagFilter, WholeReadClippedFilter
public interface SamRecordFilter
API for filtering SAMRecords $Id$

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    filterOut(SAMRecord record)
    Determines whether a SAMRecord matches this filter
    boolean
    filterOut(SAMRecord first, SAMRecord second)
    Determines whether a pair of SAMRecords matches this filter

  • Method Details

    • filterOut

      boolean filterOut(SAMRecord record)
      Determines whether a SAMRecord matches this filter
      Parameters:
      record - the SAMRecord to evaluate
      Returns:
      true if the SAMRecord matches the filter, otherwise false

    • filterOut

      boolean filterOut(SAMRecord first, SAMRecord second)
      Determines whether a pair of SAMRecords matches this filter
      Parameters:
      first - the first SAMRecord to evaluate
      second - the second SAMRecord to evaluate
      Returns:
      true if the pair of records matches filter, otherwise false