umcg.genetica.io.trityper.converters

Class VCFToTriTyper

java.lang.Object

umcg.genetica.io.trityper.converters.VCFToTriTyper

public class VCFToTriTyper
extends Object

Author:

harmjan

Constructor Summary

Constructors

Constructor and Description
VCFToTriTyper()

Method Summary

Modifier and Type	Method and Description
void	parse(String dir, String oudir) Parse and assume all variants are SNPs
void	parse(String dir, String outdir, String snpPatternString) Parser that can filter variants to only include SNPs

Methods inherited from class java.lang.Object

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

Constructor Detail

VCFToTriTyper

public VCFToTriTyper()

Method Detail

parse

public void parse(String dir,
                  String oudir)
           throws IOException

Parse and assume all variants are SNPs

Parameters:

dir -

oudir -

Throws:

IOException

parse

public void parse(String dir,
                  String outdir,
                  String snpPatternString)
           throws IOException

Parser that can filter variants to only include SNPs

Parameters:

dir -

outdir -

snpPatternString - pattern INFO column of VCF must contain. Use null for no check

Throws:

IOException