gkarrays::readsReader Class Reference

#include <readsReader.h>

List of all members.

Public Member Functions
	readsReader (char *filename, uint k=0, uint length=0)
	readsReader (char *filename1, char *filename2, uint k=0, uint length=0)
readIterator *	begin (bool printWarnings=false)
bool	isPairedEnd ()

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Detailed Description

readsReader is a class that allows you to store informations about an RNA_Seq experiment. It works both for single reads and paired-end reads. You can get an iterator using method begin() in order to go trough all reads.

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Constructor & Destructor Documentation

gkarrays::readsReader::readsReader	(	char *	filename,
		uint	k = 0,
		uint	length = 0
	)

Single reads constructor

Parameters:

filename	The name of the file containg reads
k	length of k-mers we have to use (0 for variable-length reads)
length	length of the reads. If a shorter read is found, it raises an error. If a longer read is found, only the prefix of tag_length characters is kept. If tag_length == 0 (default), just gess what the read length is.

gkarrays::readsReader::readsReader	(	char *	filename1,
		char *	filename2,
		uint	k = 0,
		uint	length = 0
	)

Single reads constructor

Parameters:

filename1	The name of the first file containing reads
filename2	The name of the second file containing reads
k	length of k-mers we have to use (0 for variable-length reads)
length	length of the reads. If a shorter read is found, it raises an error. If a longer read is found, only the prefix of tag_length characters is kept. If tag_length == 0 (default), just gess what the read length is.

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Member Function Documentation

readIterator * gkarrays::readsReader::begin

(

bool

printWarnings = false

)

Parameters:

printWarnings

Value of printWarnings option

Returns:

an read iterator that goes through the read file(s)

bool gkarrays::readsReader::isPairedEnd

(

)

Returns:

true is the reads are paired-end (i.e there is two reads files)

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

• readsReader.h
• readsReader.cpp