Package picard.sam.util

Class SamComparison

java.lang.Object
picard.sam.util.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 Details

    • 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 Details

    • writeReport

      public void writeReport(File output)

    • writeReport

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

    • getMappingsMatch

      public long getMappingsMatch()

    • getUnmappedBoth

      public long getUnmappedBoth()

    • getUnmappedLeft

      public long getUnmappedLeft()

    • getUnmappedRight

      public long getUnmappedRight()

    • getMappingsDiffer

      public long getMappingsDiffer()

    • getMissingLeft

      public long getMissingLeft()

    • getMissingRight

      public long getMissingRight()

    • getDuplicateMarkingsDiffer

      public long getDuplicateMarkingsDiffer()

    • areEqual

      public boolean areEqual()