umcg.genetica.io.fasta

Class ReferenceGenomeFasta

java.lang.Object

umcg.genetica.io.fasta.ReferenceGenomeFasta

public class ReferenceGenomeFasta
extends Object

Author:

Patrick Deelen

Field Summary

Fields

Modifier and Type	Field and Description
static Set<String>	HUMAN_NORMAL_CHR CHR 1-22, X and Y

Constructor Summary

Constructors

Constructor and Description
ReferenceGenomeFasta(File fastaFile, Set<String> chrIncludeFilter)

Method Summary

Modifier and Type	Method and Description
Set<String>	getChromosomes()
char	getNucleotide(String chr, long pos)
boolean	loadedChr(String chr)

Methods inherited from class java.lang.Object

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

Field Detail

HUMAN_NORMAL_CHR

public static final Set<String> HUMAN_NORMAL_CHR

CHR 1-22, X and Y

Constructor Detail

ReferenceGenomeFasta

public ReferenceGenomeFasta(File fastaFile,
                            Set<String> chrIncludeFilter)
                     throws IOException,
                            Exception

Throws:

IOException

Exception

Method Detail

getNucleotide

public char getNucleotide(String chr,
                          long pos)
                   throws Exception

Throws:

Exception

getChromosomes

public Set<String> getChromosomes()

loadedChr

public boolean loadedChr(String chr)