Class LibraryIdGenerator


  • public class LibraryIdGenerator
    extends Object
    A class to generate library Ids and keep duplication metrics by library IDs.
    • Constructor Detail

      • LibraryIdGenerator

        public LibraryIdGenerator​(htsjdk.samtools.SAMFileHeader header)
    • Method Detail

      • 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.
      • getNumberOfOpticalDuplicateClusters

        public long getNumberOfOpticalDuplicateClusters()