Package picard.arrays.illumina
Class CreateExtendedIlluminaManifest
java.lang.Object
picard.cmdline.CommandLineProgram
picard.arrays.illumina.CreateExtendedIlluminaManifest
Create an Extended Illumina Manifest by performing a liftover to Build 37.
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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 String[]
Put any custom command-line validation in an override of this method.protected int
doWork()
Do the work after command line has been parsed.protected ReferenceArgumentCollection
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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INPUT
@Argument(shortName="I", doc="This is the text version of the Illumina .bpm file") public File INPUT -
OUTPUT
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BAD_ASSAYS_FILE
@Argument(shortName="BAF", doc="The name of the the \'bad assays file\'. This is a subset version of the extended manifest, containing only unmappable assays", optional=true) public File BAD_ASSAYS_FILE -
REPORT_FILE
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FLAG_DUPLICATES
@Argument(shortName="FD", doc="Flag duplicates in the extended manifest. If this is set and there are multiple passing assays at the same site (same locus and alleles) then all but one will be marked with the \'DUPE\' flag in the extended manifest. The one that is not marked as \'DUPE\' will be the one with the highest Gentrain score as read from the cluster file.", optional=true) public Boolean FLAG_DUPLICATES -
CLUSTER_FILE
@Argument(shortName="CF", doc="The Standard (Hapmap-trained) cluster file (.egt) from Illumina. If there are duplicate assays at a site, this is used to decide which is the \'best\' (non-filtered in generated VCFs) by choosing the assay with the best GenTrain scores)", optional=true) public File CLUSTER_FILE -
DBSNP_FILE
@Argument(shortName="DBSNP", doc="Reference dbSNP file in VCF format.", optional=true) public File DBSNP_FILE -
TARGET_BUILD
@Argument(shortName="TB", doc="The target build. This specifies the reference for which the extended manifest will be generated. Currently this tool only supports Build 37 (Genome Reference Consortium Human Build 37 (GRCh37)). If entries are found in the Illumina manifest that are on this build they will be used with the coordinate specified in the manifest, If there are entries found on other builds, they will be marked as failed in the extended manifest UNLESS the build and liftover information (SUPPORTED_BUILD, SUPPORTED_REFERENCE_FILE, and SUPPORTED_CHAIN_FILE) is supplied.") public String TARGET_BUILD -
SUPPORTED_BUILD
@Argument(shortName="SB", doc="A supported build. The order of the input must match the order for SUPPORTED_REFERENCE_FILE and SUPPORTED_CHAIN_FILE. This is the name of the build as specified in the \'GenomeBuild\' column of the Illumina manifest file.", optional=true) public List<String> SUPPORTED_BUILD -
SUPPORTED_REFERENCE_FILE
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SUPPORTED_CHAIN_FILE
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Constructor Details
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CreateExtendedIlluminaManifest
public CreateExtendedIlluminaManifest()
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Method Details
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makeReferenceArgumentCollection
- Overrides:
makeReferenceArgumentCollection
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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customCommandLineValidation
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 classCommandLineProgram
- 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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