ReorderSam (picard 2.18.2 API)

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 dropped. Runs substantially faster if the input is an indexed BAM file.
Example
```
     java -jar picard.jar ReorderSam \
          INPUT=sample.bam \
          OUTPUT=reordered.bam \
          REFERENCE=reference_with_different_order.fasta
 
```

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class ReorderSam.ReorderSamReferenceArgumentCollection

Nested Classes
Modifier and Type	Class	Description
`static class`	`ReorderSam.ReorderSamReferenceArgumentCollection`

Field Summary

Fields
Modifier and Type Field Description

boolean ALLOW_CONTIG_LENGTH_DISCORDANCE

boolean ALLOW_INCOMPLETE_DICT_CONCORDANCE

File INPUT

File OUTPUT
- Fields inherited from class picard.cmdline.CommandLineProgram
  COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Fields
Modifier and Type	Field	Description
`boolean`	`ALLOW_CONTIG_LENGTH_DISCORDANCE`
`boolean`	`ALLOW_INCOMPLETE_DICT_CONCORDANCE`
`File`	`INPUT`
`File`	`OUTPUT`

Constructor Summary

Constructors
Constructor Description

ReorderSam()

Constructors
Constructor	Description
`ReorderSam()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected int`	`doWork()`	Do the work after command line has been parsed.
`protected ReferenceArgumentCollection`	`makeReferenceArgumentCollection()`

Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, 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 File INPUT

OUTPUT

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

ALLOW_INCOMPLETE_DICT_CONCORDANCE

@Argument(shortName="S",
          doc="If true, then 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
- makeReferenceArgumentCollection
```
protected ReferenceArgumentCollection makeReferenceArgumentCollection()
```
  Overrides:
  
  makeReferenceArgumentCollection in class CommandLineProgram
- 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.

Class ReorderSam

Summary

Example

Nested Class Summary

Field Summary

Fields inherited from class picard.cmdline.CommandLineProgram

Constructor Summary

Method Summary

Methods inherited from class picard.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Field Detail

INPUT

OUTPUT

ALLOW_INCOMPLETE_DICT_CONCORDANCE

ALLOW_CONTIG_LENGTH_DISCORDANCE

Constructor Detail

ReorderSam

Method Detail

makeReferenceArgumentCollection

doWork