Package picard.sam
Class CompareSAMs
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.CompareSAMs
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@DocumentedFeature public class CompareSAMs extends CommandLineProgram
Rudimentary SAM comparer. Compares headers, and if headers are compatible enough, compares SAMRecords, looking only at basic alignment info. Summarizes the number of alignments that match, mismatch, are missing, etc.
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Field Summary
Fields Modifier and Type Field Description List<File>
samFiles
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CompareSAMs()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
areEqual()
protected int
doWork()
Do the work after command line has been parsed.int
getMappingsDiffer()
int
getMappingsMatch()
int
getMissingLeft()
int
getMissingRight()
int
getUnmappedBoth()
int
getUnmappedLeft()
int
getUnmappedRight()
static void
main(String[] argv)
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Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Method Detail
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main
public static void main(String[] argv)
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doWork
protected int doWork()
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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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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areEqual
public boolean areEqual()
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