umcg.genetica.io.pileup

Class PileupFile

java.lang.Object

umcg.genetica.io.pileup.PileupFile

All Implemented Interfaces:

Iterable<PileupEntry>

public class PileupFile
extends Object
implements Iterable<PileupEntry>

Author:

Patrick Deelen

Constructor Summary

Constructors

Constructor and Description
PileupFile(File pileupFile, int minimumBaseQuality)
PileupFile(String pileupFilePath, int minimumBaseQuality)

Method Summary

Modifier and Type	Method and Description
String	getAbsolutePath()
Iterator<PileupEntry>	iterator()
static PileupEntry	parsePileupLine(String line, int minimumBaseQuality)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

PileupFile

public PileupFile(String pileupFilePath,
                  int minimumBaseQuality)
           throws FileNotFoundException,
                  IOException

Throws:

FileNotFoundException

IOException

PileupFile

public PileupFile(File pileupFile,
                  int minimumBaseQuality)
           throws FileNotFoundException,
                  IOException

Throws:

FileNotFoundException

IOException

Method Detail

parsePileupLine

public static PileupEntry parsePileupLine(String line,
                                          int minimumBaseQuality)
                                   throws PileupParseException

Throws:

PileupParseException

iterator

public Iterator<PileupEntry> iterator()

Specified by:

iterator in interface Iterable<PileupEntry>

getAbsolutePath

public String getAbsolutePath()