picard.fingerprint

Class CrosscheckReadGroupFingerprints

java.lang.Object

picard.cmdline.CommandLineProgram

picard.fingerprint.CrosscheckFingerprints

picard.fingerprint.CrosscheckReadGroupFingerprints

Deprecated.

6/6/2017 Use CrosscheckFingerprints instead.

@Deprecated
public class CrosscheckReadGroupFingerprints
extends CrosscheckFingerprints

Program to check that all read groups within the set of BAM files appear to come from the same individual.

Field Summary

Fields

Modifier and Type	Field and 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, NUM_THREADS, OUTPUT, OUTPUT_ERRORS_ONLY, SECOND_INPUT, SECOND_INPUT_SAMPLE_MAP, TEST_INPUT_READABILITY

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

Constructor Summary

Constructors

Constructor and Description
CrosscheckReadGroupFingerprints() Deprecated.

Method Summary

Modifier and Type	Method and Description
protected java.lang.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

getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

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.

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.

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.

Constructor Detail

CrosscheckReadGroupFingerprints

public CrosscheckReadGroupFingerprints()

Deprecated.

Method Detail

customCommandLineValidation

protected java.lang.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 class CrosscheckFingerprints

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.

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 class CrosscheckFingerprints

Returns:

program exit status.