Class AlignmentSummaryMetricsCollector


public class AlignmentSummaryMetricsCollector extends SAMRecordAndReferenceMultiLevelCollector<AlignmentSummaryMetrics,Integer>
  • Constructor Details

    • AlignmentSummaryMetricsCollector

      public AlignmentSummaryMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, boolean doRefMetrics, List<String> adapterSequence, int maxInsertSize, Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations, boolean isBisulfiteSequenced)
  • Method Details

    • makeChildCollector

      protected PerUnitMetricCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference> makeChildCollector(String sample, String library, String readGroup)
      Description copied from class: MultiLevelCollector
      Construct a PerUnitMetricCollector with the given arguments.
      Specified by:
      makeChildCollector in class MultiLevelCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
      Parameters:
      sample - If aggregating by ALL_READS this will be null, otherwise the sample that will be used to identify this collector
      library - If aggregating by SAMPLE this will be null, otherwise the library that will be used to identify this collector
      readGroup - If aggregating by LIBRARY this will be null, otherwise the readGroup that will be used to identify this collector
      Returns:
      A PerUnitMetricCollector parameterized by the given arguments
    • acceptRecord

      public void acceptRecord(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
      Description copied from class: MultiLevelCollector
      Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record
      Overrides:
      acceptRecord in class MultiLevelCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
    • get3PrimeSoftClippedBases

      protected static int get3PrimeSoftClippedBases(htsjdk.samtools.Cigar cigar, boolean negativeStrand)
      returns the length of the soft clip on the 3' end If there are no-non-clipping operators, method will return 0 as it is unclear which clips should be considered on the "3'" end.
      Parameters:
      cigar - The input Cigar of the read
      negativeStrand - the negativeStrandFlag of the read
      Returns:
      the amount of soft-clipping that the read has on its 3' end (the later read cycles)