umms.core.readers.PairedEndReader Class Reference

Classes
enum	AlignmentType

Public Member Functions
	PairedEndReader (File bam)
	PairedEndReader (File bam, TranscriptionRead read)
	PairedEndReader (File bam, TranscriptionRead read, boolean fra)
AlignmentType	getAlignmentType ()
void	setFragmentFlag (boolean fra)
void	close () throws IOException
SAMFileHeader	getHeader ()
Set< String >	getSequenceNames ()
boolean	hasIndex ()
CloseableIterator< Alignment >	iterator ()
CloseableIterator< Alignment >	query (Annotation a, boolean contained)
int	getRefSequenceLengths (String chr)
Map< String, Integer >	getRefSequenceLengths ()

Static Public Member Functions
static AlignmentType	getAlignmentType (SAMFileHeader header)
static boolean	isPairedEndFormat (String fileToCheck)
static String	getPairedEndFile (String fileToCheck)
static String	getOrCreatePairedEndFile (String fileToCheck, TranscriptionRead txnRead)
static void	main (String[] args)

Constructor & Destructor Documentation

umms.core.readers.PairedEndReader.PairedEndReader

(

File

bam

)

umms.core.readers.PairedEndReader.PairedEndReader	(	File	bam,
		TranscriptionRead	read
	)

umms.core.readers.PairedEndReader.PairedEndReader	(	File	bam,
		TranscriptionRead	read,
		boolean	fra
	)

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Member Function Documentation

void umms.core.readers.PairedEndReader.close

(

)

throws IOException

static AlignmentType umms.core.readers.PairedEndReader.getAlignmentType ( SAMFileHeader  header )

static

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AlignmentType umms.core.readers.PairedEndReader.getAlignmentType

(

)

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SAMFileHeader umms.core.readers.PairedEndReader.getHeader

(

)

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static String umms.core.readers.PairedEndReader.getOrCreatePairedEndFile ( String  fileToCheck, TranscriptionRead  txnRead  )

static

Finds a paired end file or creates one if it doesn't exist

Parameters

fileToCheck

Returns

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static String umms.core.readers.PairedEndReader.getPairedEndFile ( String  fileToCheck )

static

Returns the file itself or the file plus the default

PAIRED_END_EXTENSION 

if either is in paired end format. If neither is in paired end format, returns null.

Parameters

fileToCheck

Returns

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int umms.core.readers.PairedEndReader.getRefSequenceLengths

(

String

chr

)

Get the lengths of the reference sequences

Parameters

chr	the chromsoome to query size

Returns

Map associating each reference name with sequence length

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Map<String, Integer> umms.core.readers.PairedEndReader.getRefSequenceLengths

(

)

Get the lengths of the reference sequences

Returns

Map associating each reference name with sequence length

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Set<String> umms.core.readers.PairedEndReader.getSequenceNames

(

)

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boolean umms.core.readers.PairedEndReader.hasIndex

(

)

static boolean umms.core.readers.PairedEndReader.isPairedEndFormat ( String  fileToCheck )

static

Returns

true 

if the given SAM file is in paired end format (has the mateLine) attribute. Will also check the file with the default extension.

Parameters

fileToCheck

Returns

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CloseableIterator<Alignment> umms.core.readers.PairedEndReader.iterator

(

)

static void umms.core.readers.PairedEndReader.main ( String[]  args )

static

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CloseableIterator<Alignment> umms.core.readers.PairedEndReader.query	(	Annotation	a,
		boolean	contained
	)

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void umms.core.readers.PairedEndReader.setFragmentFlag

(

boolean

fra

)

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

• java/umms/core/readers/PairedEndReader.java