Package picard.fingerprint
Class CrosscheckReadGroupFingerprints
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.fingerprint.CrosscheckFingerprints
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- picard.fingerprint.CrosscheckReadGroupFingerprints
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@Deprecated public class CrosscheckReadGroupFingerprints extends CrosscheckFingerprints
Deprecated.6/6/2017 UseCrosscheckFingerprints
instead.Program to check that all read groups within the set of BAM files appear to come from the same individual.
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Field Summary
Fields Modifier and Type Field Description boolean
CROSSCHECK_LIBRARIES
Deprecated.boolean
CROSSCHECK_SAMPLES
Deprecated.boolean
EXPECT_ALL_READ_GROUPS_TO_MATCH
Deprecated.-
Fields inherited from class picard.fingerprint.CrosscheckFingerprints
ALLOW_DUPLICATE_READS, CALCULATE_TUMOR_AWARE_RESULTS, CROSSCHECK_BY, CROSSCHECK_MODE, EXIT_CODE_WHEN_MISMATCH, EXIT_CODE_WHEN_NO_VALID_CHECKS, EXPECT_ALL_GROUPS_TO_MATCH, GENOTYPING_ERROR_RATE, HAPLOTYPE_MAP, INPUT, INPUT_SAMPLE_FILE_MAP, INPUT_SAMPLE_MAP, LOD_THRESHOLD, LOSS_OF_HET_RATE, MATRIX_OUTPUT, MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK, NUM_THREADS, OUTPUT, OUTPUT_ERRORS_ONLY, SECOND_INPUT, SECOND_INPUT_SAMPLE_MAP, TEST_INPUT_READABILITY
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Fields 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, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CrosscheckReadGroupFingerprints()
Deprecated.
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description protected String[]
customCommandLineValidation()
Deprecated.Put any custom command-line validation in an override of this method.protected int
doWork()
Deprecated.Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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CROSSCHECK_SAMPLES
@Argument(doc="Instead of producing the normal comparison of read-groups, roll fingerprints up to the sample level and print out a sample x sample matrix with LOD scores.") public boolean CROSSCHECK_SAMPLES
Deprecated.
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CROSSCHECK_LIBRARIES
@Argument(doc="Instead of producing the normal comparison of read-groups, roll fingerprints up to the library level and print out a library x library matrix with LOD scores.") public boolean CROSSCHECK_LIBRARIES
Deprecated.
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EXPECT_ALL_READ_GROUPS_TO_MATCH
@Argument(doc="Expect all read groups\' fingerprints to match, irrespective of their sample names. By default (with this value set to false), read groups with different sample names are expected to mismatch, and those with the same sample name are expected to match.", mutex="EXPECT_ALL_GROUPS_TO_MATCH") public boolean EXPECT_ALL_READ_GROUPS_TO_MATCH
Deprecated.
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Method Detail
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customCommandLineValidation
protected String[] customCommandLineValidation()
Deprecated.Description copied from class:CommandLineProgram
Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.- Overrides:
customCommandLineValidation
in classCrosscheckFingerprints
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
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doWork
protected int doWork()
Deprecated.Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Overrides:
doWork
in classCrosscheckFingerprints
- Returns:
- program exit status.
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