Package picard.sam

Class SamComparisonMetric


  • @DocumentedFeature(groupName="Metrics",
                       summary="Metrics")
    public class SamComparisonMetric
    extends htsjdk.samtools.metrics.MetricBase
    Metric for results of SamComparison. Used to store results in CompareSAMs.
    • Field Detail

      • LEFT_FILE

        public String LEFT_FILE
        Left file used in comparison
      • RIGHT_FILE

        public String RIGHT_FILE
        Right file used in comparison
      • MAPPINGS_MATCH

        public int MAPPINGS_MATCH
        The number of primary records for which mappings match in files. If running in strict alignment mode, this counts only records which are mapped in both files with the same alignment start positions and strands. If running with LENIENT_LOW_MQ_ALIGNMENT=true, then all records which are mapped in both files with mapping quality at most equal to LOW_MQ_THRESHOLD are counted as matching. If running with LENIENT_255_MQ_ALIGNMENT=true, all records which are mapped in both files with mapping quality 255 are counted as matches.
      • MAPPINGS_DIFFER

        public int MAPPINGS_DIFFER
        The number of primary records which are mapped in both files but do not meet criteria to be counted in MAPPINGS_MATCH.
      • UNMAPPED_BOTH

        public int UNMAPPED_BOTH
        The number of primary records which are not mapped in either file.
      • UNMAPPED_LEFT

        public int UNMAPPED_LEFT
        The number of primary records which are mapped in right file and found but not mapped in left file
      • UNMAPPED_RIGHT

        public int UNMAPPED_RIGHT
        The number of primary records which are mapped in left file and found but not mapped in right file
      • MISSING_LEFT

        public int MISSING_LEFT
        The number of primary records which are found in right file but not found in left file
      • MISSING_RIGHT

        public int MISSING_RIGHT
        The number of primary records which are found in left file but not found in right file
      • DUPLICATE_MARKINGS_DIFFER

        public int DUPLICATE_MARKINGS_DIFFER
        The number of primary records for which duplicate markings are different. If running in strict duplicate marking mode, any primary alignment which is marked as a duplicate in one file but not in the other will be counted. If running with LENIENT_DUP=true, we allow for swaps between duplicate and non-duplicate fragments in the same duplicate set to reduce the number of fragments with different duplicate marking. Note that this metric is counted on a per read basis, so a paired end fragment which differs in duplicate marking between the two files will increment this metric by 2.
      • ARE_EQUAL

        public boolean ARE_EQUAL
        Whether or not to consider the two input files equal. The two input files are considered equal iff MAPPINGS_DIFFER == UNMAPPED_LEFT == UNMAPPED_RIGHT == MISSING_LEFT == MISSING_RIGHT == DUPLICATE_MARKINGS_DIFFER == 0 && the headers have been compared to be equal. Note that the header comparison result can be dependent on whether the tool is run with LENIENT_HEADER true or false.
    • Constructor Detail

      • SamComparisonMetric

        public SamComparisonMetric()