Package htsjdk.samtools.filter

Class IntervalKeepPairFilter

java.lang.Object
htsjdk.samtools.filter.IntervalKeepPairFilter
All Implemented Interfaces:
SamRecordFilter
public class IntervalKeepPairFilter extends Object implements SamRecordFilter
Filter out SAMRecords where neither record of a pair overlaps a given set of intervals. If one record of a pair overlaps the interval list, than both are kept. It is required that the SAMRecords are passed in coordinate order, have non-null SAMFileHeaders, and that Mate Cigar (MC) is present.

  • Constructor Details

    • IntervalKeepPairFilter

      public IntervalKeepPairFilter(List<Interval> intervals)
      Prepare to filter out SAMRecords that do not overlap the given list of intervals
      Parameters:
      intervals -

  • Method Details

    • filterOut

      public boolean filterOut(SAMRecord record)
      Determines whether a SAMRecord matches this filter. Takes record, finds the location of its mate using the MC tag. Checks if either record overlaps the current interval using overlap detector. If yes, return false -> don't filter it out. If a read is secondary, supplementary, or single ended, filter read out. Use IntervalFilter if you want to keep these reads, but NOTE: the resulting bam may not be valid.
      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 both SAMRecords do not overlap the interval list