Class IntervalFilter

  • All Implemented Interfaces:
    SamRecordFilter

    public class IntervalFilter
    extends Object
    implements SamRecordFilter
    Filter SAMRecords so that only those that overlap the given list of intervals. It is required that the SAMRecords are passed in coordinate order, and have non-null SAMFileHeaders. $Id$
    • Constructor Detail

      • IntervalFilter

        public IntervalFilter​(List<Interval> intervals,
                              SAMFileHeader samHeader)
        Prepare to filter out SAMRecords that do not overlap the given list of intervals
        Parameters:
        intervals - -- must be locus-ordered & non-overlapping
    • Method Detail

      • filterOut

        public boolean filterOut​(SAMRecord record)
        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