Package picard.sam.markduplicates.util

Class LibraryIdGenerator

java.lang.Object
picard.sam.markduplicates.util.LibraryIdGenerator
public class LibraryIdGenerator extends Object
A class to generate library Ids and keep duplication metrics by library IDs.

  • Constructor Details

    • LibraryIdGenerator

      public LibraryIdGenerator(htsjdk.samtools.SAMFileHeader header)

    • LibraryIdGenerator

      public LibraryIdGenerator(htsjdk.samtools.SAMFileHeader header, boolean flowMetrics)

  • Method Details

    • getLibraryIdsMap

      public Map<String,Short> getLibraryIdsMap()

    • getMetricsByLibraryMap

      public Map<String,DuplicationMetrics> getMetricsByLibraryMap()

    • getOpticalDuplicatesByLibraryIdMap

      public htsjdk.samtools.util.Histogram<Short> getOpticalDuplicatesByLibraryIdMap()

    • getDuplicateCountHist

      public htsjdk.samtools.util.Histogram<Double> getDuplicateCountHist()

    • getNonOpticalDuplicateCountHist

      public htsjdk.samtools.util.Histogram<Double> getNonOpticalDuplicateCountHist()

    • getOpticalDuplicateCountHist

      public htsjdk.samtools.util.Histogram<Double> getOpticalDuplicateCountHist()

    • getReadGroupLibraryName

      public static String getReadGroupLibraryName(htsjdk.samtools.SAMReadGroupRecord readGroup)

    • getLibraryName

      public static String getLibraryName(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.SAMRecord rec)
      Gets the library name from the header for the record. If the RG tag is not present on the record, or the library isn't denoted on the read group, a constant string is returned.

    • getLibraryId

      public short getLibraryId(htsjdk.samtools.SAMRecord rec)
      Get the library ID for the given SAM record.

    • getMetricsByLibrary

      public DuplicationMetrics getMetricsByLibrary(String library)

    • addMetricsByLibrary

      public void addMetricsByLibrary(String library, DuplicationMetrics metrics)

    • getNumberOfOpticalDuplicateClusters

      public long getNumberOfOpticalDuplicateClusters()