picard.sam

Class ReorderSam

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.ReorderSam

@DocumentedFeature
public class ReorderSam
extends CommandLineProgram

Reorders a SAM/BAM input file according to the order of contigs in a second reference file.

Summary

Not to be confused with SortSam which sorts a SAM or BAM file with a valid sequence dictionary, ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are unmapped. Runs substantially faster if the input is an indexed BAM file.

Example

     java -jar picard.jar ReorderSam \
          INPUT=sample.bam \
          OUTPUT=reordered.bam \
          SEQUENCE_DICTIONARY=reference_with_different_order.dict
 

Caveats

Note that REFERENCE_SEQUENCE is used for reading the INPUT, (e.g. when reading cram files) not for determining the order of the OUTPUT. For that you must specify the SEQUENCE_DICTIONARY argument.

Field Summary

Fields

Modifier and Type	Field and Description
boolean	ALLOW_CONTIG_LENGTH_DISCORDANCE
boolean	ALLOW_INCOMPLETE_DICT_CONCORDANCE
java.io.File	INPUT
java.io.File	OUTPUT
java.io.File	SEQUENCE_DICTIONARY

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
ReorderSam()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

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

Field Detail

INPUT

@Argument(shortName="I",
          doc="Input file (SAM or BAM) to extract reads from.")
public java.io.File INPUT

OUTPUT

@Argument(shortName="O",
          doc="Output file (SAM or BAM) to write extracted reads to.")
public java.io.File OUTPUT

SEQUENCE_DICTIONARY

@Argument(shortName="SD",
          doc="A Sequence Dictionary for the OUTPUT file (can be read from one of the following file types (SAM, BAM, VCF, BCF, Interval List, Fasta, or Dict)")
public java.io.File SEQUENCE_DICTIONARY

ALLOW_INCOMPLETE_DICT_CONCORDANCE

@Argument(shortName="S",
          doc="If true, allows only a partial overlap of the original contigs with the new reference sequence contigs.  By default, this tool requires a corresponding contig in the new reference for each read contig")
public boolean ALLOW_INCOMPLETE_DICT_CONCORDANCE

ALLOW_CONTIG_LENGTH_DISCORDANCE

@Argument(shortName="U",
          doc="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length.  Highly dangerous, only use if you know what you are doing.")
public boolean ALLOW_CONTIG_LENGTH_DISCORDANCE

Constructor Detail

ReorderSam

public ReorderSam()

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.