Package picard.sam

Class SamComparisonMetric

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.sam.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 Summary

    Fields
    Modifier and Type
    Field
    Description
    boolean
    ARE_EQUAL
    Whether or not to consider the two input files equal.
    long
    DUPLICATE_MARKINGS_DIFFER
    The number of primary records for which duplicate markings are different.
    String
    LEFT_FILE
    Left file used in comparison
    long
    MAPPINGS_DIFFER
    The number of primary records which are mapped in both files but do not meet criteria to be counted in MAPPINGS_MATCH.
    long
    MAPPINGS_MATCH
    The number of primary records for which mappings match in files.
    long
    MISSING_LEFT
    The number of primary records which are found in right file but not found in left file
    long
    MISSING_RIGHT
    The number of primary records which are found in left file but not found in right file
    String
    RIGHT_FILE
    Right file used in comparison
    long
    UNMAPPED_BOTH
    The number of primary records which are not mapped in either file.
    long
    UNMAPPED_LEFT
    The number of primary records which are mapped in right file and found but not mapped in left file
    long
    UNMAPPED_RIGHT
    The number of primary records which are mapped in left file and found but not mapped in right file

  • Constructor Summary

    Constructors
    Constructor
    Description
    SamComparisonMetric()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    allVisitedAlignmentsEqual()
     
    void
    updateMetric(SamComparison.AlignmentComparison comp)
     

    Methods inherited from class htsjdk.samtools.metrics.MetricBase

    equals, hashCode, toString

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait

  • Field Details

    • 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 long 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 long 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 long UNMAPPED_BOTH
      The number of primary records which are not mapped in either file.

    • UNMAPPED_LEFT

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

    • UNMAPPED_RIGHT

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

    • MISSING_LEFT

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

    • MISSING_RIGHT

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

    • DUPLICATE_MARKINGS_DIFFER

      public long 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 invalid input: '&'invalid input: '&' 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 Details

    • SamComparisonMetric

      public SamComparisonMetric()

  • Method Details