Package htsjdk.samtools.filter

Class TagFilter

java.lang.Object
htsjdk.samtools.filter.TagFilter
All Implemented Interfaces:
SamRecordFilter
public class TagFilter extends Object implements SamRecordFilter
Filter class for matching tag attributes in SAMRecords $Id$

  • Constructor Details

    • TagFilter

      public TagFilter(String tag, Object value)
      Constructor for a single value
      Parameters:
      tag - the key of the tag to match
      value - the value to match

    • TagFilter

      public TagFilter(String tag, List<Object> values)
      Constructor for multiple values
      Parameters:
      tag - the key of the tag to match
      values - the matching values

    • TagFilter

      public TagFilter(String tag, Object value, Boolean includeReads)
      Constructor for a single value
      Parameters:
      tag - the key of the tag to match
      value - the value to match
      includeReads - whether to include or not include reads that match filter

    • TagFilter

      public TagFilter(String tag, List<Object> values, Boolean includeReads)
      Constructor for multiple values
      Parameters:
      tag - the key of the tag to match
      values - the matching values
      includeReads - whether to include or not include reads that match filter

  • Method Details

    • 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:
      the XOR of SAMRecord matches the filter and includeReads.

    • filterOut

      public boolean filterOut(SAMRecord first, SAMRecord second)
      Determines whether a paired 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 includeReads is true and neither SAMRecord matches filter true if includeReads is false and both SAMRecords match filter otherwise false