org.dishevelled.bio.tools

Class Gfa1ToGfa2

java.lang.Object

org.dishevelled.bio.tools.Gfa1ToGfa2

All Implemented Interfaces:

Callable<Integer>

public final class Gfa1ToGfa2
extends Object
implements Callable<Integer>

Convert GFA 1.0 format to GFA 2.0 format.

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
Gfa1ToGfa2(File inputGfa1File, File outputGfa2File) Convert GFA 1.0 format to GFA 2.0 format.
Gfa1ToGfa2(Path inputGfa1Path, File outputGfa2File) Convert GFA 1.0 format to GFA 2.0 format.

Method Summary

Modifier and Type	Method and Description
Integer	call()
static void	main(String[] args) Main.
(package private) static Orientation	toGfa2Orientation(Orientation orientation)
(package private) static Reference	toGfa2Reference(Reference reference)
(package private) static List<Reference>	toGfa2References(List<Reference> references)

Methods inherited from class java.lang.Object

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

Constructor Detail

Gfa1ToGfa2

public Gfa1ToGfa2(File inputGfa1File,
                  File outputGfa2File)

Convert GFA 1.0 format to GFA 2.0 format.

Parameters:

inputGfa1File - input GFA 1.0 file, if any

outputGfa2File - output GFA 2.0 file, if any

Gfa1ToGfa2

public Gfa1ToGfa2(Path inputGfa1Path,
                  File outputGfa2File)

Convert GFA 1.0 format to GFA 2.0 format.

Parameters:

inputGfa1Path - input GFA 1.0 path, if any

outputGfa2File - output GFA 2.0 file, if any

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

Specified by:

call in interface Callable<Integer>

Throws:

Exception

toGfa2References

static List<Reference> toGfa2References(List<Reference> references)

toGfa2Reference

static Reference toGfa2Reference(Reference reference)

toGfa2Orientation

static Orientation toGfa2Orientation(Orientation orientation)

main

public static void main(String[] args)

Main.

Parameters:

args - command line args