Inheritance diagram for broad.pda.samtools.PairedEndReadIterator:

Collaboration diagram for broad.pda.samtools.PairedEndReadIterator:

Public Member Functions
	PairedEndReadIterator (SAMFileReader reader)

boolean	hasNext ()

Pair< SAMRecord >	next ()

void	close ()

void	remove ()

int	getSingleReadsSkipped ()

Detailed Description

Author: engreitz This class iterators over a standard format SAM or BAM file, but gives an iterator over paired reads with the same name. Does not return reads that do not have a mate.

Constructor & Destructor Documentation

broad.pda.samtools.PairedEndReadIterator.PairedEndReadIterator ( SAMFileReader reader )

void broad.pda.samtools.PairedEndReadIterator.close ( )

int broad.pda.samtools.PairedEndReadIterator.getSingleReadsSkipped ( )

boolean broad.pda.samtools.PairedEndReadIterator.hasNext ( )

Pair<SAMRecord> broad.pda.samtools.PairedEndReadIterator.next ( )

void broad.pda.samtools.PairedEndReadIterator.remove ( )

The documentation for this class was generated from the following file: