org.dishevelled.bio.tools

Class CompressSam

java.lang.Object

org.dishevelled.bio.tools.CompressSam

All Implemented Interfaces:

Callable<Integer>

public final class CompressSam
extends Object
implements Callable<Integer>

Compress alignments in SAM format to splittable bgzf or bzip2 compression codecs.

Since:

1.1

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
CompressSam(File inputSamFile, File outputSamFile) Compress alignments in SAM format to splittable bgzf or bzip2 compression codecs.
CompressSam(Path inputSamPath, File outputSamFile) Compress alignments in SAM format to splittable bgzf or bzip2 compression codecs.

Method Summary

Modifier and Type	Method and Description
Integer	call()
static void	main(String[] args) Main.

Methods inherited from class java.lang.Object

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

Constructor Detail

CompressSam

public CompressSam(File inputSamFile,
                   File outputSamFile)

Compress alignments in SAM format to splittable bgzf or bzip2 compression codecs.

Parameters:

inputSamFile - input SAM file, if any

outputSamFile - output SAM file, if any

CompressSam

public CompressSam(Path inputSamPath,
                   File outputSamFile)

Compress alignments in SAM format to splittable bgzf or bzip2 compression codecs.

Parameters:

inputSamPath - input SAM path, if any

outputSamFile - output SAM file, if any

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

Specified by:

call in interface Callable<Integer>

Throws:

Exception

main

public static void main(String[] args)

Main.

Parameters:

args - command line args