Package htsjdk.samtools.filter

Class SecondaryOrSupplementaryFilter

java.lang.Object
htsjdk.samtools.filter.SecondaryOrSupplementaryFilter
All Implemented Interfaces:
SamRecordFilter
public class SecondaryOrSupplementaryFilter extends Object implements SamRecordFilter
Filter out SAMRecords with Secondary or Supplementary flag set This class should be viewed as a replacement for NotPrimarySkippingIterator, in that we did not want to change the functionality of NPSI to no longer match its name $Id$

  • Constructor Details

    • SecondaryOrSupplementaryFilter

      public SecondaryOrSupplementaryFilter()

  • 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)
      Determines whether a pair of SAMRecord 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 SAMRecords matches the filter, otherwise false