Package htsjdk.samtools

Class HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter

java.lang.Object
htsjdk.samtools.HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter
All Implemented Interfaces:
SamRecordFilter
Enclosing class:
HtsgetBAMFileReader
public static class HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter extends Object implements SamRecordFilter
Filters out records that do not match any of the given intervals and query type.

  • Constructor Details

    • BAMQueryMultipleIntervalsIteratorFilter

      public BAMQueryMultipleIntervalsIteratorFilter(List<Locatable> intervals, boolean contained)

  • Method Details

    • filterOut

      public boolean filterOut(SAMRecord record)
      Description copied from interface: SamRecordFilter
      Determines whether a SAMRecord matches this filter
      Specified by:
      filterOut in interface SamRecordFilter
      Parameters:
      record - the SAMRecord to evaluate
      Returns:
      true if the SAMRecord matches the filter, otherwise false

    • filterOut

      public boolean filterOut(SAMRecord first, SAMRecord second)
      Description copied from interface: SamRecordFilter
      Determines whether a pair of SAMRecords matches this filter
      Specified by:
      filterOut in interface SamRecordFilter
      Parameters:
      first - the first SAMRecord to evaluate
      second - the second SAMRecord to evaluate
      Returns:
      true if the pair of records matches filter, otherwise false