Class CrosscheckMetric

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.fingerprint.CrosscheckMetric
Direct Known Subclasses:
ClusteredCrosscheckMetric

public class CrosscheckMetric extends htsjdk.samtools.metrics.MetricBase
A class to hold the result of crosschecking fingerprints. The same metric will be used for crosschecking Readgroups, libraries, samples, or files.
  • Field Details

    • LEFT_GROUP_VALUE

      public String LEFT_GROUP_VALUE
      The LEFT group value.
    • RIGHT_GROUP_VALUE

      public String RIGHT_GROUP_VALUE
      The RIGHT group value.
    • RESULT

      The overall result of the match.
    • DATA_TYPE

      public CrosscheckMetric.DataType DATA_TYPE
      The data type that was being compared.
    • LOD_SCORE

      public Double LOD_SCORE
      The resulting LOD score comparing LEFT and RIGHT data.
    • LOD_SCORE_TUMOR_NORMAL

      public Double LOD_SCORE_TUMOR_NORMAL
      The resulting LOD score comparing LEFT as tumor and RIGHT as normal.
    • LOD_SCORE_NORMAL_TUMOR

      public Double LOD_SCORE_NORMAL_TUMOR
      The resulting LOD score comparing LEFT as normal and RIGHT as tumor.
    • LEFT_RUN_BARCODE

      public String LEFT_RUN_BARCODE
      The LEFT run barcode (PU field) expected to look like : D047KACXX110901.1.ACCAACTG.
    • LEFT_LANE

      public Integer LEFT_LANE
      The LEFT lane.
    • LEFT_MOLECULAR_BARCODE_SEQUENCE

      public String LEFT_MOLECULAR_BARCODE_SEQUENCE
      The LEFT molecular (sample) barcode.
    • LEFT_LIBRARY

      public String LEFT_LIBRARY
      The LEFT library identifier.
    • LEFT_SAMPLE

      public String LEFT_SAMPLE
      The LEFT sample identifier.
    • LEFT_FILE

      public String LEFT_FILE
      The LEFT file from which the fingerprint was obtained.
    • RIGHT_RUN_BARCODE

      public String RIGHT_RUN_BARCODE
      The RIGHT run barcode (PU field) expected to look like : D047KACXX110901.1.ACCAACTG.
    • RIGHT_LANE

      public Integer RIGHT_LANE
      The RIGHT lane.
    • RIGHT_MOLECULAR_BARCODE_SEQUENCE

      public String RIGHT_MOLECULAR_BARCODE_SEQUENCE
      The RIGHT molecular (sample) barcode.
    • RIGHT_LIBRARY

      public String RIGHT_LIBRARY
      The RIGHT library identifier.
    • RIGHT_SAMPLE

      public String RIGHT_SAMPLE
      The RIGHT sample identifier.
    • RIGHT_FILE

      public String RIGHT_FILE
      The RIGHT file from which the fingerprint was obtained.
  • Constructor Details

    • CrosscheckMetric

      public CrosscheckMetric()