Inheritance diagram for broad.pda.samtools.SAMPairedEndFileReader:

Collaboration diagram for broad.pda.samtools.SAMPairedEndFileReader:

Public Member Functions
	SAMPairedEndFileReader (final File file)

CloseableIterator< Alignment >	iterator ()

CloseableIterator< SAMRecord >	getSAMRecordIterator ()

void	close ()

SAMFileReader	getReader ()

CloseableIterator< Alignment >	query (String sequence, int start, int end, boolean contained)

SAMFileHeader	getHeader ()

Set< String >	getSequenceNames ()

boolean	hasIndex ()

Static Public Member Functions
static SAMRecord	convertToPairedEndFragment (SAMRecord rec)

Detailed Description

Author: engreitz Modeled after the Picard SAMFileReader Currently this class does not just extend the Picard SAMFileReader because that class has a lot more functionality that would be a pain to implement in the paired-end format.

Also it's trying to accommodate iterators of both SAMRecords and Alignments to be compatible with Scripture/IGV. Annoying.

Note: With move to ScriptureV2, this class was replaced with nextgen.core.writers.PairedEndWriter and nextgen.core.readers.PairedEndReader

Constructor & Destructor Documentation

broad.pda.samtools.SAMPairedEndFileReader.SAMPairedEndFileReader ( final File file )

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

static SAMRecord broad.pda.samtools.SAMPairedEndFileReader.convertToPairedEndFragment ( SAMRecord rec )

static

SAMFileHeader broad.pda.samtools.SAMPairedEndFileReader.getHeader ( )

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SAMFileReader broad.pda.samtools.SAMPairedEndFileReader.getReader ( )

CloseableIterator<SAMRecord> broad.pda.samtools.SAMPairedEndFileReader.getSAMRecordIterator ( )

Set<String> broad.pda.samtools.SAMPairedEndFileReader.getSequenceNames ( )

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boolean broad.pda.samtools.SAMPairedEndFileReader.hasIndex ( )

CloseableIterator<Alignment> broad.pda.samtools.SAMPairedEndFileReader.iterator ( )

CloseableIterator<Alignment> broad.pda.samtools.SAMPairedEndFileReader.query	(	String	sequence,
		int	start,
		int	end,
		boolean	contained
	)

final int broad.pda.samtools.SAMPairedEndFileReader.MAX_INSERT = 2000

static

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