Package htsjdk.samtools.filter

Class OverclippedReadFilter

java.lang.Object
htsjdk.samtools.filter.OverclippedReadFilter
All Implemented Interfaces:
SamRecordFilter
public class OverclippedReadFilter extends Object implements SamRecordFilter
Filters out reads with very few unclipped bases, likely due to the read coming from a foreign organism, e.g. bacterial contamination. Based on GATK's OverclippedReadFilter.

  • Constructor Details

    • OverclippedReadFilter

      public OverclippedReadFilter(int unclippedBasesThreshold, boolean filterSingleEndClips)

  • 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