Package picard.illumina
Class IlluminaBasecallsToFastq
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- picard.cmdline.CommandLineProgram
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- picard.illumina.IlluminaBasecallsToFastq
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@DocumentedFeature public class IlluminaBasecallsToFastq extends CommandLineProgram
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
IlluminaBasecallsToFastq.ReadNameFormat
Simple switch to control the read name format to emit.
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Field Summary
Fields Modifier and Type Field Description List<IlluminaUtil.IlluminaAdapterPair>
ADAPTERS_TO_CHECK
Deprecated.boolean
APPLY_EAMSS_FILTER
File
BARCODES_DIR
File
BASECALLS_DIR
boolean
COMPRESS_OUTPUTS
Integer
FIRST_TILE
String
FLOWCELL_BARCODE
Boolean
FORCE_GC
boolean
IGNORE_UNEXPECTED_BARCODES
boolean
INCLUDE_NON_PF_READS
Integer
LANE
String
MACHINE_NAME
int
MAX_READS_IN_RAM_PER_TILE
int
MINIMUM_QUALITY
File
MULTIPLEX_PARAMS
Integer
NUM_PROCESSORS
File
OUTPUT_PREFIX
IlluminaBasecallsToFastq.ReadNameFormat
READ_NAME_FORMAT
String
READ_STRUCTURE
String
RUN_BARCODE
Integer
TILE_LIMIT
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, 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 IlluminaBasecallsToFastq()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected String[]
customCommandLineValidation()
Put any custom command-line validation in an override of this method.protected int
doWork()
Do the work after command line has been parsed.static void
main(String[] args)
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Methods inherited from class picard.cmdline.CommandLineProgram
getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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BASECALLS_DIR
@Argument(doc="The basecalls directory. ", shortName="B") public File BASECALLS_DIR
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BARCODES_DIR
@Argument(doc="The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If not set, use BASECALLS_DIR. ", shortName="BCD", optional=true) public File BARCODES_DIR
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LANE
@Argument(doc="Lane number. ", shortName="L") public Integer LANE
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OUTPUT_PREFIX
@Argument(doc="The prefix for output FASTQs. Extensions as described above are appended. Use this option for a non-barcoded run, or for a barcoded run in which it is not desired to demultiplex reads into separate files by barcode.", shortName="O", mutex="MULTIPLEX_PARAMS") public File OUTPUT_PREFIX
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RUN_BARCODE
@Argument(doc="The barcode of the run. Prefixed to read names.") public String RUN_BARCODE
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MACHINE_NAME
@Argument(doc="The name of the machine on which the run was sequenced; required if emitting Casava1.8-style read name headers", optional=true) public String MACHINE_NAME
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FLOWCELL_BARCODE
@Argument(doc="The barcode of the flowcell that was sequenced; required if emitting Casava1.8-style read name headers", optional=true) public String FLOWCELL_BARCODE
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READ_STRUCTURE
@Argument(doc="A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the input data consists of 80 base clusters and we provide a read structure of \"28T8M8B8S28T\" then the sequence may be split up into four reads:\n* read one with 28 cycles (bases) of template\n* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)\n* read three with 8 cycles (bases) of sample barcode\n* 8 cycles (bases) skipped.\n* read four with 28 cycles (bases) of template\nThe skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein.", shortName="RS") public String READ_STRUCTURE
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MULTIPLEX_PARAMS
@Argument(doc="Tab-separated file for creating all output FASTQs demultiplexed by barcode for a lane with single IlluminaBasecallsToFastq invocation. The columns are OUTPUT_PREFIX, and BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster (optional). Row with BARCODE_1 set to \'N\' is used to specify an output_prefix for no barcode match.", mutex="OUTPUT_PREFIX") public File MULTIPLEX_PARAMS
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ADAPTERS_TO_CHECK
@Deprecated @Argument(doc="Deprecated (No longer used). Which adapters to look for in the read.", optional=true) public List<IlluminaUtil.IlluminaAdapterPair> ADAPTERS_TO_CHECK
Deprecated.
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NUM_PROCESSORS
@Argument(doc="The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0, then the number of cores used will be the number available on the machine less NUM_PROCESSORS.") public Integer NUM_PROCESSORS
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FIRST_TILE
@Argument(doc="If set, this is the first tile to be processed (used for debugging). Note that tiles are not processed in numerical order.", optional=true) public Integer FIRST_TILE
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TILE_LIMIT
@Argument(doc="If set, process no more than this many tiles (used for debugging).", optional=true) public Integer TILE_LIMIT
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APPLY_EAMSS_FILTER
@Argument(doc="Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of reads and convert their quality scores to Q2.") public boolean APPLY_EAMSS_FILTER
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FORCE_GC
@Argument(doc="If true, call System.gc() periodically. This is useful in cases in which the -Xmx value passed is larger than the available memory.") public Boolean FORCE_GC
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MAX_READS_IN_RAM_PER_TILE
@Argument(doc="Configure SortingCollections to store this many records before spilling to disk. For an indexed run, each SortingCollection gets this value/number of indices.") public int MAX_READS_IN_RAM_PER_TILE
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MINIMUM_QUALITY
@Argument(doc="The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are lower than this value, an error is thrown.The default of 2 is what the Illumina\'s spec describes as the minimum, but in practice the value has been observed lower.") public int MINIMUM_QUALITY
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INCLUDE_NON_PF_READS
@Argument(doc="Whether to include non-PF reads", shortName="NONPF", optional=true) public boolean INCLUDE_NON_PF_READS
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IGNORE_UNEXPECTED_BARCODES
@Argument(doc="Whether to ignore reads whose barcodes are not found in MULTIPLEX_PARAMS. Useful when outputting FASTQs for only a subset of the barcodes in a lane.", shortName="INGORE_UNEXPECTED") public boolean IGNORE_UNEXPECTED_BARCODES
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READ_NAME_FORMAT
@Argument(doc="The read name header formatting to emit. Casava1.8 formatting has additional information beyond Illumina, including: the passing-filter flag value for the read, the flowcell name, and the sequencer name.") public IlluminaBasecallsToFastq.ReadNameFormat READ_NAME_FORMAT
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COMPRESS_OUTPUTS
@Argument(shortName="GZIP", doc="Compress output FASTQ files using gzip and append a .gz extension to the file names.") public boolean COMPRESS_OUTPUTS
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Method Detail
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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
protected String[] 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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main
public static void main(String[] args)
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