org.opencb.cellbase.lib.builders.utils

Class GenomeSequenceUtils

java.lang.Object

org.opencb.cellbase.lib.builders.utils.GenomeSequenceUtils

public class GenomeSequenceUtils
extends Object

Created with IntelliJ IDEA. User: imedina Date: 9/25/13 Time: 12:06 PM To change this template use File | Settings | File Templates.

Constructor Summary

Constructors

Constructor and Description
GenomeSequenceUtils()

Method Summary

Modifier and Type	Method and Description
static String	getChromosomeSequence(String chromosome, Path genomeSequencePath)
static String	getChromosomeSequenceFromFiles(String chrom, Path genomeSequenceDir)
static Map<String,String>	getGenomeSequence(Path genomeSequencePath)
static Map<String,byte[]>	getGenomeSequenceGZipped(Path genomeSequencePath)

Methods inherited from class java.lang.Object

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

Constructor Detail

GenomeSequenceUtils

public GenomeSequenceUtils()

Method Detail

getGenomeSequence

public static Map<String,String> getGenomeSequence(Path genomeSequencePath)
                                            throws IOException

Throws:

IOException

getGenomeSequenceGZipped

public static Map<String,byte[]> getGenomeSequenceGZipped(Path genomeSequencePath)
                                                   throws IOException

Throws:

IOException

getChromosomeSequence

public static String getChromosomeSequence(String chromosome,
                                           Path genomeSequencePath)
                                    throws IOException

Throws:

IOException

getChromosomeSequenceFromFiles

public static String getChromosomeSequenceFromFiles(String chrom,
                                                    Path genomeSequenceDir)
                                             throws IOException

Throws:

IOException