uk.ac.sanger.npg.picard
Class BamReadTrimmer

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

public class BamReadTrimmer
extends PicardCommandLine

The class to strip part of a read (fixed position) - typically a prefix of the forward read, and optionally place this and its quality in BAM tags.

Field Summary

java.lang.Integer	FIRST_POSITION_TO_TRIM
java.io.File	INPUT
java.lang.Boolean	ONLY_FORWARD_READ
java.io.File	OUTPUT
java.lang.Boolean	SAVE_TRIM
java.util.List<java.lang.String>	TAG_TO_KEEP
java.lang.String	TRIM_BASE_TAG
java.lang.Integer	TRIM_LENGTH
java.lang.String	TRIM_QUALITY_TAG
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

BamReadTrimmer()

Method Summary

protected int	doWork()
static void	main(java.lang.String[] args) example: INPUT=testdata/bam/6210_8.sam OUTPUT=testdata/6210_8_trimmed.bam FIRST_POSITION_TO_TRIM=1 TRIM_LENGTH=3 CREATE_MD5_FILE=true ONLY_FORWARD_READ=true SAVE_TRIM=true TRIM_BASE_TAG=rs TRIM_QUALITY_TAG=qs VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT INPUT=testdata/bam/6210_8.sam OUTPUT=testdata/6210_8_trimmed.bam FIRST_POSITION_TO_TRIM=1 TRIM_LENGTH=3 TMP_DIR=testdata CREATE_MD5_FILE=true ONLY_FORWARD_READ=true SAVE_TRIM=true TRIM_BASE_TAG=rs TRIM_QUALITY_TAG=qs VALIDATION_STRINGENCY=SILENT
net.sf.samtools.SAMRecord	removeAlignment(net.sf.samtools.SAMRecord record, net.sf.samtools.SAMFileHeader header)
net.sf.samtools.SAMRecord	trimSAMRecord(net.sf.samtools.SAMRecord record, int firstPos, int trimLength, boolean saveTrim)

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

INPUT

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

OUTPUT

@Option(shortName="O",
        doc="The output file after trimming.")
public java.io.File OUTPUT

ONLY_FORWARD_READ

@Option(shortName="FORWARD",
        doc="Just trim the forward read if true.")
public java.lang.Boolean ONLY_FORWARD_READ

FIRST_POSITION_TO_TRIM

@Option(shortName="POS",
        doc="First position to be trimmed.")
public java.lang.Integer FIRST_POSITION_TO_TRIM

TRIM_LENGTH

@Option(shortName="LEN",
        doc="The lenght to be trimmed.")
public java.lang.Integer TRIM_LENGTH

SAVE_TRIM

@Option(shortName="SAVE",
        doc="Timmed bases to be saved?",
        optional=true)
public java.lang.Boolean SAVE_TRIM

TRIM_BASE_TAG

@Option(shortName="RS",
        doc="Tag name to be used for timmed bases.",
        optional=true)
public java.lang.String TRIM_BASE_TAG

TRIM_QUALITY_TAG

@Option(shortName="QS",
        doc="Tag name to be used for timmed qualities.",
        optional=true)
public java.lang.String TRIM_QUALITY_TAG

TAG_TO_KEEP

@Option(shortName="TAG",
        doc="A list of tags to keep.")
public final java.util.List<java.lang.String> TAG_TO_KEEP

Constructor Detail

BamReadTrimmer

public BamReadTrimmer()

Method Detail

doWork

protected int doWork()

Specified by:

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

removeAlignment

public net.sf.samtools.SAMRecord removeAlignment(net.sf.samtools.SAMRecord record,
                                                 net.sf.samtools.SAMFileHeader header)

Parameters:

record -

header -

Returns:

trimSAMRecord

public net.sf.samtools.SAMRecord trimSAMRecord(net.sf.samtools.SAMRecord record,
                                               int firstPos,
                                               int trimLength,
                                               boolean saveTrim)

Parameters:

record -

firstPos -

trimLength -

saveTrim -

Returns:

main

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

example: INPUT=testdata/bam/6210_8.sam OUTPUT=testdata/6210_8_trimmed.bam FIRST_POSITION_TO_TRIM=1 TRIM_LENGTH=3 CREATE_MD5_FILE=true ONLY_FORWARD_READ=true SAVE_TRIM=true TRIM_BASE_TAG=rs TRIM_QUALITY_TAG=qs VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT INPUT=testdata/bam/6210_8.sam OUTPUT=testdata/6210_8_trimmed.bam FIRST_POSITION_TO_TRIM=1 TRIM_LENGTH=3 TMP_DIR=testdata CREATE_MD5_FILE=true ONLY_FORWARD_READ=true SAVE_TRIM=true TRIM_BASE_TAG=rs TRIM_QUALITY_TAG=qs VALIDATION_STRINGENCY=SILENT

Parameters:

args -