Class AlignmentSummaryMetricsCollector

    • Constructor Detail

      • 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 Detail

      • 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)