Package picard.sam.util

Class SamComparison

  • public final class SamComparison
extends Object
    Compare two SAM/BAM files. Compares headers, and if headers are compatible enough, compares SAMRecords, looking at alignment and duplicate marking info. Can perform either a naive comparison for which each alignment must be identical, or a more sophisticated check of "equivalence", where mapping quality 0 reads are allowed to have different alignments, and duplicate marks are allowed to differ to account for ambiguities in selecting the representative read of a duplicate set. Results of comparison are summarised in an output metrics file.

    • Constructor Detail

      • SamComparison

        public SamComparison​(htsjdk.samtools.SamReader leftReader,
                     htsjdk.samtools.SamReader rightReader)
        Note: the caller must make sure the SamReaders are closed properly.

      • SamComparison

        public SamComparison​(htsjdk.samtools.SamReader leftReader,
                     htsjdk.samtools.SamReader rightReader,
                     String leftName,
                     String rightName,
                     SAMComparisonArgumentCollection samComparisonArgumentCollection)

    • Method Detail

      • writeReport

        public void writeReport​(File output)

      • writeReport

        public void writeReport​(File output,
                        List<htsjdk.samtools.metrics.Header> headers)

      • getMappingsMatch

        public int getMappingsMatch()

      • getUnmappedBoth

        public int getUnmappedBoth()

      • getUnmappedLeft

        public int getUnmappedLeft()

      • getUnmappedRight

        public int getUnmappedRight()

      • getMappingsDiffer

        public int getMappingsDiffer()

      • getMissingLeft

        public int getMissingLeft()

      • getMissingRight

        public int getMissingRight()

      • getDuplicateMarkingsDiffer

        public int getDuplicateMarkingsDiffer()

      • areEqual

        public boolean areEqual()