uk.ac.sanger.npg.picard
Class BamMerger

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

public class BamMerger
extends PicardCommandLine

A command-line tool to merge BAM/SAM alignment info in a bam with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM. All the fields in each read will be added if not already in alignment. The failed quality check flag in unmapped reads, and paired, first and second read flags will be added to alignment. Two bam files must be in the same order but unmapped bam may have more records than the aligned bam. There is an option to add these extra reads into final bam. Only SQ records and alignment PG in the aligned bam file will be added to the output by default. Default alignment PG ID is bwa, you need specify this PG ID from command line if not. There is an option you can merge all other PGs in aligned bam file into the output. All header information in the unmapped bam header will be kept, except SQ records.

Field Summary

java.io.File	ALIGNED_BAM
java.lang.String	ALIGNMENT_PROGRAM_ID
java.io.File	INPUT
java.lang.Boolean	KEEP_ALL_PG
java.lang.Boolean	KEEP_EXTRA_UNMAPPED_READS
java.io.File	OUTPUT
java.lang.Boolean	REPLACE_ALIGNED_BASE_QUALITY
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

BamMerger()

Method Summary

protected int	doWork()
static void	main(java.lang.String[] args) example: ALIGNED=testdata/bam/6210_8_aligned.sam I=testdata/bam/6210_8.sam OUTPUT=testdata/6210_8_merged.bam TMP_DIR=testdata VALIDATION_STRINGENCY=SILENT
void	mergeRecords(net.sf.samtools.SAMRecord alignment, net.sf.samtools.SAMRecord record)

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

ALIGNED_BAM

@Option(shortName="ALIGNED",
        doc="The input SAM or BAM file with alignment.")
public java.io.File ALIGNED_BAM

ALIGNMENT_PROGRAM_ID

@Option(shortName="PG",
        doc="The alignment program ID in the header of the SAM or BAM file with alignment.")
public java.lang.String ALIGNMENT_PROGRAM_ID

KEEP_ALL_PG

@Option(shortName="KEEP_PG",
        doc="keep all other PGs in aligned bam into output")
public java.lang.Boolean KEEP_ALL_PG

INPUT

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

OUTPUT

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

KEEP_EXTRA_UNMAPPED_READS

@Option(shortName="KEEP",
        doc="KEEP extra unmapped reads in unmapped bam file to the final output if true.")
public java.lang.Boolean KEEP_EXTRA_UNMAPPED_READS

REPLACE_ALIGNED_BASE_QUALITY

@Option(shortName="REPLACE_QUAL",
        doc="Replace base qualities in aligned bam wtih the ones in unaligned bam if true.")
public java.lang.Boolean REPLACE_ALIGNED_BASE_QUALITY

Constructor Detail

BamMerger

public BamMerger()

Method Detail

doWork

protected int doWork()

Specified by:

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

mergeRecords

public void mergeRecords(net.sf.samtools.SAMRecord alignment,
                         net.sf.samtools.SAMRecord record)

Parameters:

alignment -

record -

main

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

example: ALIGNED=testdata/bam/6210_8_aligned.sam I=testdata/bam/6210_8.sam OUTPUT=testdata/6210_8_merged.bam TMP_DIR=testdata VALIDATION_STRINGENCY=SILENT

Parameters:

args -