picard.illumina

Class ExtractIlluminaBarcodes

java.lang.Object

picard.cmdline.CommandLineProgram

picard.illumina.ExtractIlluminaBarcodes

public class ExtractIlluminaBarcodes
extends CommandLineProgram

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

Author:

jburke@broadinstitute.org

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ExtractIlluminaBarcodes.BarcodeMetric Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<java.lang.String>	BARCODE
java.io.File	BARCODE_FILE
java.io.File	BASECALLS_DIR
boolean	COMPRESS_OUTPUTS
java.lang.Integer	LANE
int	MAX_MISMATCHES
int	MAX_NO_CALLS
java.io.File	METRICS_FILE
int	MIN_MISMATCH_DELTA
int	MINIMUM_BASE_QUALITY
int	MINIMUM_QUALITY
int	NUM_PROCESSORS
java.io.File	OUTPUT_DIR
java.lang.String	READ_STRUCTURE

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
ExtractIlluminaBarcodes()

Method Summary

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Validate that POSITION >= 1, and that all BARCODEs are the same length and unique
protected int	doWork() Do the work after command line has been parsed.
static void	finalizeMetrics(java.util.Map<java.lang.String,ExtractIlluminaBarcodes.BarcodeMetric> barcodeToMetrics, ExtractIlluminaBarcodes.BarcodeMetric noMatchMetric)
static void	main(java.lang.String[] argv)

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

BASECALLS_DIR

@Option(doc="The Illumina basecalls directory. ",
        shortName="B")
public java.io.File BASECALLS_DIR

OUTPUT_DIR

@Option(doc="Where to write _barcode.txt files.  By default, these are written to BASECALLS_DIR.",
        optional=true)
public java.io.File OUTPUT_DIR

LANE

@Option(doc="Lane number. ",
        shortName="L")
public java.lang.Integer LANE

READ_STRUCTURE

@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

BARCODE

@Option(doc="Barcode sequence.  These must be unique, and all the same length.  This cannot be used with reads that have more than one barcode; use BARCODE_FILE in that case. ",
        mutex="BARCODE_FILE")
public java.util.List<java.lang.String> BARCODE

BARCODE_FILE

@Option(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_1\', \'barcode_sequence_2\' (optional), \'barcode_name\', and \'library_name\'.",
        mutex="BARCODE")
public java.io.File BARCODE_FILE

METRICS_FILE

@Option(doc="Per-barcode and per-lane metrics written to this file.",
        shortName="M")
public java.io.File METRICS_FILE

MAX_MISMATCHES

@Option(doc="Maximum mismatches for a barcode to be considered a match.")
public int MAX_MISMATCHES

MIN_MISMATCH_DELTA

@Option(doc="Minimum difference between number of mismatches in the best and second best barcodes for a barcode to be considered a match.")
public int MIN_MISMATCH_DELTA

MAX_NO_CALLS

@Option(doc="Maximum allowable number of no-calls in a barcode read before it is considered unmatchable.")
public int MAX_NO_CALLS

MINIMUM_BASE_QUALITY

@Option(shortName="Q",
        doc="Minimum base quality. Any barcode bases falling below this quality will be considered a mismatch even in the bases match.")
public int MINIMUM_BASE_QUALITY

MINIMUM_QUALITY

@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

COMPRESS_OUTPUTS

@Option(shortName="GZIP",
        doc="Compress output s_l_t_barcode.txt files using gzip and append a .gz extension to the file names.")
public boolean COMPRESS_OUTPUTS

NUM_PROCESSORS

@Option(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

Constructor Detail

ExtractIlluminaBarcodes

public ExtractIlluminaBarcodes()

Method Detail

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 class CommandLineProgram

Returns:

program exit status.

finalizeMetrics

public static void finalizeMetrics(java.util.Map<java.lang.String,ExtractIlluminaBarcodes.BarcodeMetric> barcodeToMetrics,
                                   ExtractIlluminaBarcodes.BarcodeMetric noMatchMetric)

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Validate that POSITION >= 1, and that all BARCODEs are the same length and unique

Overrides:

customCommandLineValidation in class CommandLineProgram

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.

main

public static void main(java.lang.String[] argv)