Package picard.sam.markduplicates

Class MarkDuplicatesForFlowHelper

java.lang.Object
picard.sam.markduplicates.MarkDuplicatesForFlowHelper
All Implemented Interfaces:
MarkDuplicatesHelper
public class MarkDuplicatesForFlowHelper extends Object implements MarkDuplicatesHelper
MarkDuplicates calculation helper class for flow based mode The class extends the behavior of MarkDuplicates which contains the complete code for the non-flow based mode. When in flow mode, additional parameters may control the establishment of read ends (start/end) for the purpose of determining duplication status. Additionally, the logic used to gather reads into (duplicate) buckets (chunks) is enhanced with an optional mechanism of read end uncertainty threshold. When active, reads are considered to belong to the same chunk if for each read in the chunk there exists at least one other read with the uncertainty distance on the read end.

  • Field Details

    • CLIPPING_TAG_NAME

      public static final String CLIPPING_TAG_NAME
      See Also:

    • CLIPPING_TAG_CONTAINS_A

      public static final char[] CLIPPING_TAG_CONTAINS_A

    • CLIPPING_TAG_CONTAINS_AQ

      public static final char[] CLIPPING_TAG_CONTAINS_AQ

    • CLIPPING_TAG_CONTAINS_QZ

      public static final char[] CLIPPING_TAG_CONTAINS_QZ

  • Constructor Details

    • MarkDuplicatesForFlowHelper

      public MarkDuplicatesForFlowHelper(MarkDuplicates md)

  • Method Details

    • generateDuplicateIndexes

      public void generateDuplicateIndexes(boolean useBarcodes, boolean indexOpticalDuplicates)
      This method is identical in function to generateDuplicateIndexes except that it accomodates for the possible significance of the end side of the reads (w/ or w/o uncertainty). This is only applicable for flow mode invocation.
      Specified by:
      generateDuplicateIndexes in interface MarkDuplicatesHelper

    • buildReadEnds

      public ReadEndsForMarkDuplicates buildReadEnds(htsjdk.samtools.SAMFileHeader header, long index, htsjdk.samtools.SAMRecord rec, boolean useBarcodes)
      Builds a read ends object that represents a single read - for flow based read
      Specified by:
      buildReadEnds in interface MarkDuplicatesHelper

    • getReadDuplicateScore

      public short getReadDuplicateScore(htsjdk.samtools.SAMRecord rec, ReadEndsForMarkDuplicates pairedEnds)
      update score for pairedEnds
      Specified by:
      getReadDuplicateScore in interface MarkDuplicatesHelper

    • getFlowSumOfBaseQualities

      protected static int getFlowSumOfBaseQualities(htsjdk.samtools.SAMRecord rec, int threshold)
      A quality summing scoring strategy used for flow based reads. The method walks on the bases of the read, in the synthesis direction. For each base, the effective quality value is defined as the value on the first base on the hmer to which the base belongs to. The score is defined to be the sum of all effective values above a given threshold.
      Parameters:
      rec - - SAMRecord to get a score for
      threshold - - threshold above which effective quality is included
      Returns:
      - calculated score (see method description)

    • getReadEndCoordinate

      protected static int getReadEndCoordinate(htsjdk.samtools.SAMRecord rec, boolean startEnd, boolean certain, MarkDuplicatesForFlowArgumentCollection flowBasedArguments)

    • isAdapterClipped

      public static boolean isAdapterClipped(htsjdk.samtools.SAMRecord rec)

    • isAdapterClippedWithQ

      public static boolean isAdapterClippedWithQ(htsjdk.samtools.SAMRecord rec)

    • isQualityClipped

      public static boolean isQualityClipped(htsjdk.samtools.SAMRecord rec)