picard.sam

Class MergeSamFiles

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.MergeSamFiles

public class MergeSamFiles
extends CommandLineProgram

Reads a SAM or BAM file and combines the output to one file

Author:

Tim Fennell

Field Summary

Fields

Modifier and Type	Field and Description
boolean	ASSUME_SORTED
java.util.List<java.lang.String>	COMMENT
java.util.List<java.io.File>	INPUT
java.io.File	INTERVALS
boolean	MERGE_SEQUENCE_DICTIONARIES
java.io.File	OUTPUT
htsjdk.samtools.SAMFileHeader.SortOrder	SORT_ORDER
boolean	USE_THREADING

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
MergeSamFiles()

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() Combines multiple SAM/BAM files into one.
static void	main(java.lang.String[] argv) Required main method implementation.

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(shortName="I",
        doc="SAM or BAM input file",
        minElements=1)
public java.util.List<java.io.File> INPUT

OUTPUT

@Option(shortName="O",
        doc="SAM or BAM file to write merged result to")
public java.io.File OUTPUT

SORT_ORDER

@Option(shortName="SO",
        doc="Sort order of output file",
        optional=true)
public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER

ASSUME_SORTED

@Option(doc="If true, assume that the input files are in the same sort order as the requested output sort order, even if their headers say otherwise.",
        shortName="AS")
public boolean ASSUME_SORTED

MERGE_SEQUENCE_DICTIONARIES

@Option(shortName="MSD",
        doc="Merge the sequence dictionaries",
        optional=true)
public boolean MERGE_SEQUENCE_DICTIONARIES

USE_THREADING

@Option(doc="Option to create a background thread to encode, compress and write to disk the output file. The threaded version uses about 20% more CPU and decreases runtime by ~20% when writing out a compressed BAM file.")
public boolean USE_THREADING

COMMENT

@Option(doc="Comment(s) to include in the merged output file\'s header.",
        optional=true,
        shortName="CO")
public java.util.List<java.lang.String> COMMENT

INTERVALS

@Option(shortName="RGN",
        doc="An interval list file that contains the locations of the positions to merge. Assume bam are sorted and indexed. The resulting file will contain alignments that may overlap with genomic regions outside the requested region. Unmapped reads are discarded.",
        optional=true)
public java.io.File INTERVALS

Constructor Detail

MergeSamFiles

public MergeSamFiles()

Method Detail

main

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

Required main method implementation.

doWork

protected int doWork()

Combines multiple SAM/BAM files into one.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.

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.