ScatterIntervalsByNs (picard 2.18.2 API)

java.lang.Object
- picard.cmdline.CommandLineProgram
- - picard.util.ScatterIntervalsByNs

```
@DocumentedFeature
public class ScatterIntervalsByNs
extends CommandLineProgram
```
A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.

Summary
Used for creating a broken-up interval list that can be used for scattering a variant-calling pipeline in a way that will not cause problems at the edges of the intervals. By using large enough N blocks (so that the tools will not be able to anchor on both sides) we can be assured that the results of scattering and gathering the variants with the resulting interval list will be the same as calling with one large region.

Input
A reference file to use for creating the intervals
Which type of intervals to emit in the output (Ns only, ACGT only or both).
An integer indicating the largest number of Ns in a contiguous block that will be "tolerated" and not converted into an N block.

Output

Usage example

Create an interval list of intervals that do not contain any N blocks for use with haplotype caller on short reads

 java -jar picard.jar ScatterIntervalsByNs \
       R=reference_sequence.fasta \
       OT=BOTH \
       O=output.interval_list

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection

Nested Classes
Modifier and Type	Class	Description
`static class`	`ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection`

Field Summary

Fields
Modifier and Type Field Description

int MAX_TO_MERGE

File OUTPUT

picard.util.ScatterIntervalsByNs.OutputType OUTPUT_TYPE
- 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
`int`	`MAX_TO_MERGE`
`File`	`OUTPUT`
`picard.util.ScatterIntervalsByNs.OutputType`	`OUTPUT_TYPE`

Constructor Summary

Constructors
Constructor Description

ScatterIntervalsByNs()

Constructors
Constructor	Description
`ScatterIntervalsByNs()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected int`	`doWork()`	Do the work after command line has been parsed.
`static void`	`main(String[] args)`
`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

OUTPUT

@Argument(shortName="O",
          doc="Output file for interval list.")
public File OUTPUT

OUTPUT_TYPE

@Argument(shortName="OT",
          doc="Type of intervals to output.",
          optional=true)
public picard.util.ScatterIntervalsByNs.OutputType OUTPUT_TYPE

MAX_TO_MERGE

@Argument(shortName="N",
          doc="Maximal number of contiguous N bases to tolerate, thereby continuing the current ACGT interval.",
          optional=true)
public int MAX_TO_MERGE

Constructor Detail
- ScatterIntervalsByNs
```
public ScatterIntervalsByNs()
```

Method Detail
- main
```
public static void main(String[] args)
```
- 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 ScatterIntervalsByNs

Summary

Input

Output

Usage example

Create an interval list of intervals that do not contain any N blocks for use with haplotype caller on short reads

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

OUTPUT

OUTPUT_TYPE

MAX_TO_MERGE

Constructor Detail

ScatterIntervalsByNs

Method Detail

main

makeReferenceArgumentCollection

doWork