umms.core.writers.PairedEndWriter Class Reference

Collaboration diagram for umms.core.writers.PairedEndWriter:

Public Member Functions
	PairedEndWriter (File bamFile)
	PairedEndWriter (File bamFile, String output)
void	setMaxAllowableInsert (int x)
void	convertInputToPairedEnd ()
void	convertInputToPairedEnd (TranscriptionRead txnRead)
String	getOutputFile ()
void	addAlignment (final Alignment alignment)
void	addRecord (final SAMRecord record)
void	close ()

Static Public Member Functions
static String	getDefaultFile (String file)

Static Public Attributes
static String	PAIRED_END_EXTENSION = ".PairedEnd.bam"
static final String	mateSequenceFlag ="ms"
static final String	mateCigarFlag ="mc"
static final String	readStartFlag ="rs"
static final String	readCigarFlag ="rc"
static final String	mateLineFlag ="mateLine"

Constructor & Destructor Documentation

umms.core.writers.PairedEndWriter.PairedEndWriter

(

File

bamFile

)

Parameters

bamFile

Input SAM or BAM file to extract header and/or reads from.

Here is the call graph for this function:

umms.core.writers.PairedEndWriter.PairedEndWriter	(	File	bamFile,
		String	output
	)

Parameters

bamFile	Input SAM or BAM file to extract header and/or reads from.
output	Output path

Member Function Documentation

void umms.core.writers.PairedEndWriter.addAlignment

(

final Alignment

alignment

)

Write a single Alignment

Parameters

alignment

Here is the call graph for this function:

void umms.core.writers.PairedEndWriter.addRecord

(

final SAMRecord

record

)

Here is the caller graph for this function:

void umms.core.writers.PairedEndWriter.close

(

)

Here is the caller graph for this function:

void umms.core.writers.PairedEndWriter.convertInputToPairedEnd

(

)

Convert the bamFile provided in the constructor to paired end format. If no transcription read is supplied, set to unstranded

void umms.core.writers.PairedEndWriter.convertInputToPairedEnd

(

TranscriptionRead

txnRead

)

Convert the bamFile provided in the constructor to paired end format. Convert the bamFile provided in the constructor to paired end format.

Here is the call graph for this function:

static String umms.core.writers.PairedEndWriter.getDefaultFile ( String  file )

static

Here is the caller graph for this function:

String umms.core.writers.PairedEndWriter.getOutputFile

(

)

void umms.core.writers.PairedEndWriter.setMaxAllowableInsert

(

int

x

)

Member Data Documentation

final String umms.core.writers.PairedEndWriter.mateCigarFlag ="mc"

static

final String umms.core.writers.PairedEndWriter.mateLineFlag ="mateLine"

static

final String umms.core.writers.PairedEndWriter.mateSequenceFlag ="ms"

static

Writes a file to represent a BAM file where the paired end reads are concatenated We will represent the basic alignment start and end for the whole fragment The attributes will have information for the component parts

String umms.core.writers.PairedEndWriter.PAIRED_END_EXTENSION = ".PairedEnd.bam"

static

final String umms.core.writers.PairedEndWriter.readCigarFlag ="rc"

static

final String umms.core.writers.PairedEndWriter.readStartFlag ="rs"

static

---

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

• java/umms/core/writers/PairedEndWriter.java