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)
ReferenceGenomeFasta(File fastaFile, Set<String> chrIncludeFilter)

Method Summary

Modifier and Type	Method and Description
Set<String>	getChromosomes()
char	getNucleotide(String chr, long pos)
StringBuilder	getNucleotides(String chr, long posStart, long posStop)
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

ReferenceGenomeFasta

public ReferenceGenomeFasta(File fastaFile)
                     throws IOException,
                            Exception

Throws:

IOException

Exception

Method Detail

getNucleotide

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

Throws:

Exception

getNucleotides

public StringBuilder getNucleotides(String chr,
                                    long posStart,
                                    long posStop)
                             throws Exception

Throws:

Exception

getChromosomes

public Set<String> getChromosomes()

loadedChr

public boolean loadedChr(String chr)