Package picard.fingerprint
Class IdentifyContaminant
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.fingerprint.IdentifyContaminant
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public class IdentifyContaminant extends CommandLineProgram
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
Fields Modifier and Type Field Description double
CONTAMINATION
boolean
EXTRACT_CONTAMINATED
File
HAPLOTYPE_MAP
String
INPUT
int
LOCUS_MAX_READS
File
OUTPUT
String
SAMPLE_ALIAS
boolean
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 IdentifyContaminant()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.protected boolean
requiresReference()
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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 Detail
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INPUT
@Argument(shortName="I", doc="Input SAM or BAM file.") public String INPUT
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OUTPUT
@Argument(shortName="O", doc="Output fingerprint file (VCF).") public File 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
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CONTAMINATION
@Argument(shortName="C", doc="A value of estimated contamination in the input. ", minValue=0.0, maxValue=1.0) public double CONTAMINATION
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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
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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
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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
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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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Method Detail
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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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