Package picard.illumina
Class ExtractIlluminaBarcodes
java.lang.Object
picard.cmdline.CommandLineProgram
picard.illumina.ExtractBarcodesProgram
picard.illumina.ExtractIlluminaBarcodes
Determine the barcode for each read in an Illumina lane.
For each tile, a file is written to the basecalls directory of the form s___barcode.txt.
An output file contains a line for each read in the tile, aligned with the regular basecall output
The output file contains the following tab-separated columns:
- read subsequence at barcode position
- Y or N indicating if there was a barcode match
- matched barcode sequence (empty if read did not match one of the barcodes). If there is no match
but we're close to the threshold of calling it a match we output the barcode that would have been
matched but in lower case
- distance to best matching barcode, "mismatches" (*)
- distance to second-best matching barcode, "mismatchesToSecondBest" (*)
NOTE (*): Due to an optimization the reported mismatches & mismatchesToSecondBest values may be inaccurate as long as
the conclusion (match vs. no-match) isn't affected. For example, reported mismatches and
mismatchesToSecondBest may be smaller than their true value if mismatches is truly larger than MAX_MISMATCHES.
Also, mismatchesToSecondBest might be smaller than its true value if its true value is greater than
mismatches + MIN_MISMATCH_DELTA.
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
Extracts barcodes and accumulates metrics for an entire tile. -
Field Summary
FieldsModifier and TypeFieldDescriptionint
Fields inherited from class picard.illumina.ExtractBarcodesProgram
BARCODE_COLUMN, BARCODE_NAME_COLUMN, BARCODE_PREFIXES, BARCODE_SEQUENCE_COLUMN, barcodeToMetrics, BASECALLS_DIR, bclQualityEvaluationStrategy, COMPRESS_OUTPUTS, DISTANCE_MODE, INPUT_PARAMS_FILE, inputReadStructure, LANE, LIBRARY_NAME_COLUMN, MAX_MISMATCHES, MAX_NO_CALLS, METRICS_FILE, MIN_MISMATCH_DELTA, MINIMUM_BASE_QUALITY, MINIMUM_QUALITY, noMatchMetric, READ_STRUCTURE
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
Methods inherited from class picard.illumina.ExtractBarcodesProgram
collectErrorMessages, createBarcodeExtractor, finalizeMetrics, outputMetrics, parseInputFile
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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BARCODE_FILE
@Argument(doc="Tab-delimited file of barcode sequences, barcode name and, optionally, library name. Barcodes must be unique and all the same length. Column headers must be \'barcode_sequence\' (or \'barcode_sequence_1\'), \'barcode_sequence_2\' (optional), \'barcode_name\', and \'library_name\'.", mutex="BARCODE") public File BARCODE_FILE -
BARCODE
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NUM_PROCESSORS
@Argument(doc="Run this many PerTileBarcodeExtractors 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 int NUM_PROCESSORS -
OUTPUT_DIR
@Argument(doc="Where to write _barcode.txt files. By default, these are written to BASECALLS_DIR.", optional=true) public File OUTPUT_DIR
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Constructor Details
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ExtractIlluminaBarcodes
public ExtractIlluminaBarcodes()
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Method Details
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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:ExtractBarcodesProgram
Parses all barcodes from input files and validates all barcodes are the same length and unique- Overrides:
customCommandLineValidation
in classExtractBarcodesProgram
- 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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