picard.fastq

Class BamToBfq

java.lang.Object

picard.cmdline.CommandLineProgram

picard.fastq.BamToBfq

public class BamToBfq
extends CommandLineProgram

CommandLineProgram to generate to bfq files for use by the Maq aligner

Author:

ktibbett@broadinstitute.org

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	ANALYSIS_DIR
java.lang.Integer	BASES_TO_WRITE
boolean	CLIP_ADAPTERS
java.lang.String	FLOWCELL_BARCODE
java.lang.Boolean	INCLUDE_NON_PF_READS
java.io.File	INPUT
java.lang.Integer	LANE
java.lang.String	OUTPUT_FILE_PREFIX
java.lang.Boolean	PAIRED_RUN
java.lang.Integer	READ_CHUNK_SIZE
java.lang.String	READ_NAME_PREFIX
java.lang.Integer	READS_TO_ALIGN
java.lang.String	RUN_BARCODE

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
BamToBfq()

Method Summary

Modifier and Type	Method and Description
protected java.lang.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(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

INPUT

@Option(doc="The BAM file to parse.",
        shortName="I")
public java.io.File INPUT

ANALYSIS_DIR

@Option(doc="The analysis directory for the binary output file. ")
public java.io.File ANALYSIS_DIR

FLOWCELL_BARCODE

@Option(doc="Flowcell barcode (e.g. 30PYMAAXX).  ",
        shortName="F",
        mutex="OUTPUT_FILE_PREFIX")
public java.lang.String FLOWCELL_BARCODE

LANE

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

OUTPUT_FILE_PREFIX

@Option(doc="Prefix for all output files",
        mutex={"FLOWCELL_BARCODE","LANE"})
public java.lang.String OUTPUT_FILE_PREFIX

READS_TO_ALIGN

@Option(doc="Number of reads to align (null = all).",
        shortName="NUM",
        optional=true)
public java.lang.Integer READS_TO_ALIGN

READ_CHUNK_SIZE

@Option(doc="Number of reads to break into individual groups for alignment",
        shortName="CHUNK")
public java.lang.Integer READ_CHUNK_SIZE

PAIRED_RUN

@Option(doc="Whether this is a paired-end run. ",
        shortName="PE")
public java.lang.Boolean PAIRED_RUN

RUN_BARCODE

@Option(doc="Deprecated option; use READ_NAME_PREFIX instead",
        mutex="READ_NAME_PREFIX",
        shortName="RB",
        optional=true)
public java.lang.String RUN_BARCODE

READ_NAME_PREFIX

@Option(doc="Prefix to be stripped off the beginning of all read names  (to make them short enough to run in Maq)",
        optional=true)
public java.lang.String READ_NAME_PREFIX

INCLUDE_NON_PF_READS

@Option(doc="Whether to include non-PF reads",
        shortName="NONPF",
        optional=true)
public java.lang.Boolean INCLUDE_NON_PF_READS

CLIP_ADAPTERS

@Option(doc="Whether to clip adapters from the reads")
public boolean CLIP_ADAPTERS

BASES_TO_WRITE

@Option(doc="The number of bases from each read to write to the bfq file.  If this is non-null, then only the first BASES_TO_WRITE bases from each read will be written.",
        optional=true)
public java.lang.Integer BASES_TO_WRITE

Constructor Detail

BamToBfq

public BamToBfq()

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.

main

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

customCommandLineValidation

protected java.lang.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 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.