Class TagFilter

    • Constructor Detail

      • 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 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:
        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