Package picard.sam.util
Class SamComparison
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- picard.sam.util.SamComparison
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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.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
SamComparison.AlignmentComparison
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Constructor Summary
Constructors Constructor Description SamComparison(htsjdk.samtools.SamReader leftReader, htsjdk.samtools.SamReader rightReader)
Note: the caller must make sure the SamReaders are closed properly.SamComparison(htsjdk.samtools.SamReader leftReader, htsjdk.samtools.SamReader rightReader, String leftName, String rightName, SAMComparisonArgumentCollection samComparisonArgumentCollection)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
areEqual()
int
getDuplicateMarkingsDiffer()
int
getMappingsDiffer()
int
getMappingsMatch()
int
getMissingLeft()
int
getMissingRight()
int
getUnmappedBoth()
int
getUnmappedLeft()
int
getUnmappedRight()
void
writeReport(File output)
void
writeReport(File output, List<htsjdk.samtools.metrics.Header> headers)
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Constructor Detail
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SamComparison
public SamComparison(htsjdk.samtools.SamReader leftReader, htsjdk.samtools.SamReader rightReader)
Note: the caller must make sure the SamReaders are closed properly.
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SamComparison
public SamComparison(htsjdk.samtools.SamReader leftReader, htsjdk.samtools.SamReader rightReader, String leftName, String rightName, SAMComparisonArgumentCollection samComparisonArgumentCollection)
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Method Detail
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writeReport
public void writeReport(File output)
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getMappingsMatch
public int getMappingsMatch()
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getUnmappedBoth
public int getUnmappedBoth()
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getUnmappedLeft
public int getUnmappedLeft()
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getUnmappedRight
public int getUnmappedRight()
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getMappingsDiffer
public int getMappingsDiffer()
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getMissingLeft
public int getMissingLeft()
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getMissingRight
public int getMissingRight()
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getDuplicateMarkingsDiffer
public int getDuplicateMarkingsDiffer()
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areEqual
public boolean areEqual()
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