Package htsjdk.samtools.filter

Class SecondaryAlignmentFilter

java.lang.Object
htsjdk.samtools.filter.SecondaryAlignmentFilter
All Implemented Interfaces:
SamRecordFilter
Direct Known Subclasses:
NotPrimaryAlignmentFilter
public class SecondaryAlignmentFilter extends Object implements SamRecordFilter
SamRecordFilter that filters out secondary alignments, but not supplemental alignments.

  • Constructor Details

    • SecondaryAlignmentFilter

      public SecondaryAlignmentFilter()

  • Method Details

    • filterOut

      public boolean filterOut(SAMRecord record)
      Returns true if the read is marked as secondary.
      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)
      Returns true if either read is marked as secondary.
      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