broad.pda.seq.fastq.FastqSplitterByBarcode Class Reference

Collaboration diagram for broad.pda.seq.fastq.FastqSplitterByBarcode:

Public Member Functions
	FastqSplitterByBarcode (String bcFile) throws IOException
void	stop () throws IOException
void	start (String pair1Source, String outputDir, String pair2Source) throws IOException
boolean	hasMore ()
boolean	isPaired ()
void	setPaired (boolean paired)
boolean	isAtEnd ()
void	setAtEnd (boolean atEnd)
int	getRead2Trim5p ()
void	setRead2Trim5p (int read2Trim5p)
int	getRead2Trim3p ()
void	setRead2Trim3p (int read2Trim3p)
int	getRead1Trim3p ()
void	setRead1Trim3p (int read1Trim3p)
int	getRead1Trim5p ()
void	setRead1Trim5p (int read1Trim5p)
boolean	isAddToReadName ()
void	setAddToReadName (boolean addToReadName)

Static Public Member Functions
static void	main (String[] args) throws Exception

Protected Member Functions
void	updateReadInfoWithBarcode (FastqSequence read, String bc)
FastqParser	getPair1Parser ()
void	setPair1Parser (FastqParser pair1Parser)
FastqParser	getPair2Parser ()
void	setPair2Parser (FastqParser pair2Parser)

Detailed Description

Reads through a fastq file and writes records to different files depending on the barcode found within the start or end of the read. Reads are trimmed to remove the barcode.

Author

mgarber

Constructor & Destructor Documentation

broad.pda.seq.fastq.FastqSplitterByBarcode.FastqSplitterByBarcode

(

String

bcFile

)

throws IOException

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Member Function Documentation

FastqParser broad.pda.seq.fastq.FastqSplitterByBarcode.getPair1Parser ( )

protected

FastqParser broad.pda.seq.fastq.FastqSplitterByBarcode.getPair2Parser ( )

protected

int broad.pda.seq.fastq.FastqSplitterByBarcode.getRead1Trim3p

(

)

int broad.pda.seq.fastq.FastqSplitterByBarcode.getRead1Trim5p

(

)

int broad.pda.seq.fastq.FastqSplitterByBarcode.getRead2Trim3p

(

)

int broad.pda.seq.fastq.FastqSplitterByBarcode.getRead2Trim5p

(

)

boolean broad.pda.seq.fastq.FastqSplitterByBarcode.hasMore

(

)

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boolean broad.pda.seq.fastq.FastqSplitterByBarcode.isAddToReadName

(

)

boolean broad.pda.seq.fastq.FastqSplitterByBarcode.isAtEnd

(

)

boolean broad.pda.seq.fastq.FastqSplitterByBarcode.isPaired

(

)

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static void broad.pda.seq.fastq.FastqSplitterByBarcode.main ( String[]  args ) throws Exception

static

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void broad.pda.seq.fastq.FastqSplitterByBarcode.setAddToReadName

(

boolean

addToReadName

)

void broad.pda.seq.fastq.FastqSplitterByBarcode.setAtEnd

(

boolean

atEnd

)

void broad.pda.seq.fastq.FastqSplitterByBarcode.setPair1Parser ( FastqParser  pair1Parser )

protected

void broad.pda.seq.fastq.FastqSplitterByBarcode.setPair2Parser ( FastqParser  pair2Parser )

protected

void broad.pda.seq.fastq.FastqSplitterByBarcode.setPaired

(

boolean

paired

)

void broad.pda.seq.fastq.FastqSplitterByBarcode.setRead1Trim3p

(

int

read1Trim3p

)

void broad.pda.seq.fastq.FastqSplitterByBarcode.setRead1Trim5p

(

int

read1Trim5p

)

void broad.pda.seq.fastq.FastqSplitterByBarcode.setRead2Trim3p

(

int

read2Trim3p

)

void broad.pda.seq.fastq.FastqSplitterByBarcode.setRead2Trim5p

(

int

read2Trim5p

)

void broad.pda.seq.fastq.FastqSplitterByBarcode.start	(	String	pair1Source,
		String	outputDir,
		String	pair2Source
	)		throws IOException

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void broad.pda.seq.fastq.FastqSplitterByBarcode.stop

(

)

throws IOException

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void broad.pda.seq.fastq.FastqSplitterByBarcode.updateReadInfoWithBarcode ( FastqSequence  read, String  bc  )

protected

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

• java/broad/pda/seq/fastq/FastqSplitterByBarcode.java