Package picard.sam.util
Class SamComparison
java.lang.Object
picard.sam.util.SamComparison
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 -
Constructor Summary
ConstructorsConstructorDescriptionSamComparison
(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) -
Method Summary
Modifier and TypeMethodDescriptionboolean
areEqual()
int
int
int
int
int
int
int
int
void
writeReport
(File output) void
writeReport
(File output, List<htsjdk.samtools.metrics.Header> headers)
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Constructor Details
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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. -
SamComparison
public SamComparison(htsjdk.samtools.SamReader leftReader, htsjdk.samtools.SamReader rightReader, String leftName, String rightName, SAMComparisonArgumentCollection samComparisonArgumentCollection)
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Method Details
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writeReport
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writeReport
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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()
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