org.utgenome.format.sam
Class SAMReadIterator

java.lang.Object
  org.utgenome.format.sam.SAMReadIterator

All Implemented Interfaces:

Iterator<SAMRead>

public class SAMReadIterator
extends Object
implements Iterator<SAMRead>

Iterator for SAM entries

Author:

leo

Constructor Summary

SAMReadIterator(File bamFile, String chr)

SAMReadIterator(File bamFile, String chr, int start, int end)

Method Summary

static Iterator<SAMRead>	getIteratorOnChr(File bamFile, String chr)
static Iterator<SAMRead>	getOverlappingIterator(File bamFile, ChrLoc loc)
boolean	hasNext()
SAMRead	next()
void	remove()

Methods inherited from class java.lang.Object

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

Constructor Detail

SAMReadIterator

public SAMReadIterator(File bamFile,
                       String chr)

SAMReadIterator

public SAMReadIterator(File bamFile,
                       String chr,
                       int start,
                       int end)

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator<SAMRead>

next

public SAMRead next()

Specified by:

next in interface Iterator<SAMRead>

remove

public void remove()

Specified by:

remove in interface Iterator<SAMRead>

getIteratorOnChr

public static Iterator<SAMRead> getIteratorOnChr(File bamFile,
                                                 String chr)

getOverlappingIterator

public static Iterator<SAMRead> getOverlappingIterator(File bamFile,
                                                       ChrLoc loc)