Package picard.fingerprint
Class IdentifyContaminant
java.lang.Object
picard.cmdline.CommandLineProgram
picard.fingerprint.IdentifyContaminant
Program to create a fingerprint for the contaminating sample when the level of contamination is both known and
uniform in the genome.
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Field Summary
FieldsModifier and TypeFieldDescriptiondouble
boolean
int
boolean
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, 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.protected boolean
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser
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Field Details
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INPUT
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OUTPUT
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HAPLOTYPE_MAP
@Argument(shortName="H", doc="A file of haplotype information. The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.") public File HAPLOTYPE_MAP -
CONTAMINATION
@Argument(shortName="C", doc="A value of estimated contamination in the input. ", minValue=0.0, maxValue=1.0) public double CONTAMINATION -
SAMPLE_ALIAS
@Argument(doc="The sample alias to associate with the resulting fingerprint. When null, <SAMPLE> is extracted from the input file and \"<SAMPLE>-contamination\" is used.", optional=true) public String SAMPLE_ALIAS -
LOCUS_MAX_READS
@Argument(doc="The maximum number of reads to use as evidence for any given locus. This is provided as a way to limit the effect that any given locus may have.") public int LOCUS_MAX_READS -
EXTRACT_CONTAMINATED
@Argument(doc="Extract a fingerprint for the contaminated sample (instead of the contaminant). Setting to true changes the effect of SAMPLE_ALIAS when null. It names the sample in the VCF <SAMPLE>, using the SM value from the SAM header.") public boolean EXTRACT_CONTAMINATED -
TEST_INPUT_READABILITY
@Hidden @Argument(doc="When true code will check for readability on input files (this can be slow on cloud access)") public boolean TEST_INPUT_READABILITY
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Constructor Details
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IdentifyContaminant
public IdentifyContaminant()
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Method Details
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requiresReference
protected boolean requiresReference()- Overrides:
requiresReference
in classCommandLineProgram
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doWork
protected int doWork()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.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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