uk.ac.sanger.npg.illumina
Class Illumina2bam

java.lang.Object
  net.sf.picard.cmdline.CommandLineProgram
      uk.ac.sanger.npg.picard.PicardCommandLine
          uk.ac.sanger.npg.illumina.Illumina2bam

public class Illumina2bam
extends PicardCommandLine

This is the main class to convert Illumina BCL files to BAM

Field Summary

java.lang.String	BARCODE_QUALITY_TAG_NAME
java.lang.String	BARCODE_SEQUENCE_TAG_NAME
java.io.File	BASECALLS_DIR
java.lang.Integer	FIRST_TILE
boolean	GENERATE_SECONDARY_BASE_CALLS
java.io.File	INTENSITY_DIR
java.lang.Integer	LANE
java.lang.String	LIBRARY_NAME
java.io.File	OUTPUT
boolean	PF_FILTER
java.lang.String	PLATFORM
java.lang.String	PLATFORM_UNIT
java.lang.String	READ_GROUP_ID
java.io.File	RUN_FOLDER
net.sf.samtools.util.Iso8601Date	RUN_START_DATE
java.lang.String	SAMPLE_ALIAS
java.lang.String	SECOND_BARCODE_QUALITY_TAG_NAME
java.lang.String	SECOND_BARCODE_SEQUENCE_TAG_NAME
java.lang.String	SEQUENCING_CENTER
java.lang.String	STUDY_NAME
java.lang.Integer	TILE_LIMIT
java.lang.String	USAGE

Fields inherited from class uk.ac.sanger.npg.picard.PicardCommandLine

version

Fields inherited from class net.sf.picard.cmdline.CommandLineProgram

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

Constructor Summary

Illumina2bam()

Method Summary

protected int	doWork()
net.sf.samtools.SAMReadGroupRecord	generateSamReadGroupRecord(java.lang.String platformUnitConfig, java.util.Date runDateConfig) Generate read group record
static void	main(java.lang.String[] args)

Methods inherited from class uk.ac.sanger.npg.picard.PicardCommandLine

addProgramRecordToHead, getThisProgramRecord, makeUniqueProgramId

Methods inherited from class net.sf.picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getProgramVersion, getStandardUsagePreamble, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

USAGE

@Usage(programVersion="1.00")
public final java.lang.String USAGE

RUN_FOLDER

@Option(shortName="R",
        doc="Illumina runfolder directory including runParameters xml file under it, upwards two levels from Intensities directory if not given.",
        optional=true)
public java.io.File RUN_FOLDER

INTENSITY_DIR

@Option(shortName="I",
        doc="Illumina intensities directory including config xml file, and clocs, locs or pos files under lane directory.")
public java.io.File INTENSITY_DIR

BASECALLS_DIR

@Option(shortName="B",
        doc="Illumina basecalls directory including config xml file, and filter files, bcl, maybe scl files under lane cycle directory, using BaseCalls directory under intensities if not given. ",
        optional=true)
public java.io.File BASECALLS_DIR

LANE

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

OUTPUT

@Option(shortName="O",
        doc="Output file name.")
public java.io.File OUTPUT

GENERATE_SECONDARY_BASE_CALLS

@Option(shortName="E2",
        doc="Including second base call or not, default false.",
        optional=true)
public boolean GENERATE_SECONDARY_BASE_CALLS

PF_FILTER

@Option(shortName="PF",
        doc="Filter cluster or not, default true.",
        optional=true)
public boolean PF_FILTER

READ_GROUP_ID

@Option(shortName="RG",
        doc="ID used to link RG header record with RG tag in SAM record, default 1.",
        optional=true)
public java.lang.String READ_GROUP_ID

SAMPLE_ALIAS

@Option(shortName="SM",
        doc="The name of the sequenced sample, using library name if not given.",
        optional=true)
public java.lang.String SAMPLE_ALIAS

LIBRARY_NAME

@Option(shortName="LB",
        doc="The name of the sequenced library, default unknown.",
        optional=true)
public java.lang.String LIBRARY_NAME

STUDY_NAME

@Option(shortName="ST",
        doc="The name of the study.",
        optional=true)
public java.lang.String STUDY_NAME

PLATFORM_UNIT

@Option(shortName="PU",
        doc="The platform unit, using runfolder name plus lane number if not given.",
        optional=true)
public java.lang.String PLATFORM_UNIT

RUN_START_DATE

@Option(doc="The start date of the run, read from config file if not given.",
        optional=true)
public net.sf.samtools.util.Iso8601Date RUN_START_DATE

SEQUENCING_CENTER

@Option(shortName="SC",
        doc="Sequence center name, default SC for Sanger Center.",
        optional=true)
public java.lang.String SEQUENCING_CENTER

PLATFORM

@Option(doc="The name of the sequencing technology that produced the read, default ILLUMINA.",
        optional=true)
public java.lang.String PLATFORM

FIRST_TILE

@Option(doc="If set, this is the first tile to be processed (for debugging).  Note that tiles are not processed in numerical order.",
        optional=true)
public java.lang.Integer FIRST_TILE

TILE_LIMIT

@Option(doc="If set, process no more than this many tiles (for debugging).",
        optional=true)
public java.lang.Integer TILE_LIMIT

BARCODE_SEQUENCE_TAG_NAME

@Option(shortName="BC_SEQ",
        doc="Tag name for barcode sequence.")
public java.lang.String BARCODE_SEQUENCE_TAG_NAME

BARCODE_QUALITY_TAG_NAME

@Option(shortName="BC_QUAL",
        doc="Tag name for barcode quality.")
public java.lang.String BARCODE_QUALITY_TAG_NAME

SECOND_BARCODE_SEQUENCE_TAG_NAME

@Option(shortName="SEC_BC_SEQ",
        doc="Tag name for second  barcode sequence.",
        optional=true)
public java.lang.String SECOND_BARCODE_SEQUENCE_TAG_NAME

SECOND_BARCODE_QUALITY_TAG_NAME

@Option(shortName="SEC_BC_QUAL",
        doc="Tag name for second barcode quality.",
        optional=true)
public java.lang.String SECOND_BARCODE_QUALITY_TAG_NAME

Constructor Detail

Illumina2bam

public Illumina2bam()

Method Detail

doWork

protected int doWork()

Specified by:

doWork in class net.sf.picard.cmdline.CommandLineProgram

generateSamReadGroupRecord

public net.sf.samtools.SAMReadGroupRecord generateSamReadGroupRecord(java.lang.String platformUnitConfig,
                                                                     java.util.Date runDateConfig)

Generate read group record

Parameters:

platformUnitConfig - default platform unit from configure XML, which will be used if not given from command line, and could be null

runDateConfig - default run date from configure XML, which will be used if not given from command line, and could be null

Returns:

read group record for BAM header

main

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

Parameters:

args - example INTENSITY_DIR=testdata/110323_HS13_06000_B_B039WABXX/Data/Intensities BASECALLS_DIR=testdata/110323_HS13_06000_B_B039WABXX/Data/Intensities/BaseCalls LANE=1 OUTPUT=testdata/6000_1.sam VALIDATION_STRINGENCY=STRICT CREATE_INDEX=false CREATE_MD5_FILE=true FIRST_TILE=1101 COMPRESSION_LEVEL=1 TILE_LIMIT=1