Package picard.sam
Class CompareSAMs
java.lang.Object
picard.cmdline.CommandLineProgram
picard.sam.CompareSAMs
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
FieldsModifier and TypeFieldDescriptionFields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected int
doWork()
Do the work after command line has been parsed.Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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SAM_FILES
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OUTPUT
@Argument(shortName="O", doc="Output file to write comparison results to.", optional=true) public File OUTPUT -
samComparisonArgumentCollection
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Constructor Details
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CompareSAMs
public CompareSAMs()
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Method Details
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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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