Class BarcodeMetric


  • public class BarcodeMetric
    extends htsjdk.samtools.metrics.MetricBase
    Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.
    • Field Detail

      • BARCODE

        public String BARCODE
        The barcode (from the set of expected barcodes) for which the following metrics apply. Note that the "symbolic" barcode of NNNNNN is used to report metrics for all reads that do not match a barcode.
      • BARCODE_WITHOUT_DELIMITER

        public String BARCODE_WITHOUT_DELIMITER
      • BARCODE_NAME

        public String BARCODE_NAME
        The barcode name.
      • LIBRARY_NAME

        public String LIBRARY_NAME
        The name of the library
      • READS

        public long READS
        The total number of reads matching the barcode.
      • PF_READS

        public long PF_READS
        The number of PF reads matching this barcode (always less than or equal to READS).
      • PERFECT_MATCHES

        public long PERFECT_MATCHES
        The number of all reads matching this barcode that matched with 0 errors or no-calls.
      • PF_PERFECT_MATCHES

        public long PF_PERFECT_MATCHES
        The number of PF reads matching this barcode that matched with 0 errors or no-calls.
      • ONE_MISMATCH_MATCHES

        public long ONE_MISMATCH_MATCHES
        The number of all reads matching this barcode that matched with 1 error or no-call.
      • PF_ONE_MISMATCH_MATCHES

        public long PF_ONE_MISMATCH_MATCHES
        The number of PF reads matching this barcode that matched with 1 error or no-call.
      • PCT_MATCHES

        public double PCT_MATCHES
        The fraction of all reads in the lane that matched to this barcode.
      • RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT

        public double RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT
        The rate of all reads matching this barcode to all reads matching the most prevalent barcode. For the most prevalent barcode this will be 1, for all others it will be less than 1 (except for the possible exception of when there are more orphan reads than for any other barcode, in which case the value may be arbitrarily large). One over the lowest number in this column gives you the fold-difference in representation between barcodes.
      • PF_PCT_MATCHES

        public double PF_PCT_MATCHES
        The fraction of PF reads in the lane that matched to this barcode.
      • PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT

        public double PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT
        The rate of PF reads matching this barcode to PF reads matching the most prevalent barcode. For the most prevalent barcode this will be 1, for all others it will be less than 1 (except for the possible exception of when there are more orphan reads than for any other barcode, in which case the value may be arbitrarily large). One over the lowest number in this column gives you the fold-difference in representation of PF reads between barcodes.
      • PF_NORMALIZED_MATCHES

        public double PF_NORMALIZED_MATCHES
        The "normalized" matches to each barcode. This is calculated as the number of pf reads matching this barcode over the sum of all pf reads matching any barcode (excluding orphans). If all barcodes are represented equally this will be 1.
      • barcodeBytes

        protected byte[][] barcodeBytes
    • Constructor Detail

      • BarcodeMetric

        public BarcodeMetric​(String barcodeName,
                             String libraryName,
                             String barcodeDisplay,
                             String[] barcodeSeqs)
      • BarcodeMetric

        public BarcodeMetric()
        This ctor is necessary for when reading metrics from file
    • Method Detail

      • copy

        public BarcodeMetric copy()
        Creates a copy of metric initialized with only non-accumulated and non-calculated values set
      • merge

        public void merge​(BarcodeMetric metric)
        Adds the non-calculated