public class IlluminaBasecallsToFastq extends CommandLineProgram
Modifier and Type | Class and Description |
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static class |
IlluminaBasecallsToFastq.ReadNameFormat
Simple switch to control the read name format to emit.
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Modifier and Type | Field and Description |
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java.util.List<IlluminaUtil.IlluminaAdapterPair> |
ADAPTERS_TO_CHECK |
boolean |
APPLY_EAMSS_FILTER |
java.io.File |
BARCODES_DIR |
java.io.File |
BASECALLS_DIR |
boolean |
COMPRESS_OUTPUTS |
java.lang.Integer |
FIRST_TILE |
java.lang.String |
FLOWCELL_BARCODE |
java.lang.Boolean |
FORCE_GC |
boolean |
IGNORE_UNEXPECTED_BARCODES |
boolean |
INCLUDE_NON_PF_READS |
java.lang.Integer |
LANE |
java.lang.String |
MACHINE_NAME |
int |
MAX_READS_IN_RAM_PER_TILE |
int |
MINIMUM_QUALITY |
java.io.File |
MULTIPLEX_PARAMS |
java.lang.Integer |
NUM_PROCESSORS |
java.io.File |
OUTPUT_PREFIX |
IlluminaBasecallsToFastq.ReadNameFormat |
READ_NAME_FORMAT |
java.lang.String |
READ_STRUCTURE |
java.lang.String |
RUN_BARCODE |
java.lang.Integer |
TILE_LIMIT |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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IlluminaBasecallsToFastq() |
Modifier and Type | Method and Description |
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protected java.lang.String[] |
customCommandLineValidation()
Put any custom command-line validation in an override of this method.
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protected int |
doWork()
Do the work after command line has been parsed.
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static void |
main(java.lang.String[] args) |
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(doc="The basecalls directory. ", shortName="B") public java.io.File BASECALLS_DIR
@Option(doc="The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If not set, use BASECALLS_DIR. ", shortName="BCD", optional=true) public java.io.File BARCODES_DIR
@Option(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 java.io.File OUTPUT_PREFIX
@Option(doc="The barcode of the run. Prefixed to read names.", optional=false) public java.lang.String RUN_BARCODE
@Option(doc="The name of the machine on which the run was sequenced; required if emitting Casava1.8-style read name headers", optional=true) public java.lang.String MACHINE_NAME
@Option(doc="The barcode of the flowcell that was sequenced; required if emitting Casava1.8-style read name headers", optional=true) public java.lang.String FLOWCELL_BARCODE
@Option(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 java.lang.String READ_STRUCTURE
@Option(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 java.io.File MULTIPLEX_PARAMS
@Option(doc="Which adapters to look for in the read.") public java.util.List<IlluminaUtil.IlluminaAdapterPair> ADAPTERS_TO_CHECK
@Option(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 java.lang.Integer NUM_PROCESSORS
@Option(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 java.lang.Integer FIRST_TILE
@Option(doc="If set, process no more than this many tiles (used for debugging).", optional=true) public java.lang.Integer TILE_LIMIT
@Option(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
@Option(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 java.lang.Boolean FORCE_GC
@Option(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
@Option(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
@Option(doc="Whether to include non-PF reads", shortName="NONPF", optional=true) public boolean INCLUDE_NON_PF_READS
@Option(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
@Option(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.", optional=false) public IlluminaBasecallsToFastq.ReadNameFormat READ_NAME_FORMAT
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
protected java.lang.String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram
public static void main(java.lang.String[] args)