readsRetrieval.h File Reference

#include "utils.h"
#include "indexManagementFastq.h"
#include "gzIndex.h"

Include dependency graph for readsRetrieval.h:

Go to the source code of this file.

Functions
vector< string >	retrieveReadsWithBarcodeBits_Stream (ifstream &in, BarcodesIndex &BarcodesIndex, barcode bc)
vector< string >	retrieveReadsWithBarcodeBits (string fastqFile, BarcodesIndex &BarcodesIndex, barcode bc)
vector< string >	retrieveReadsWithBarcode_Stream (ifstream &reader, BarcodesIndex &BarcodesIndex, string bc)
vector< string >	retrieveReadsWithBarcode (string fastqFile, BarcodesIndex &BarcodesIndex, string bc)
vector< string >	retrieveReadsWithBarcodes_Stream (ifstream &in, BarcodesIndex &BarcodesIndex, string barcodesList)
vector< string >	retrieveReadsWithBarcodes (string fastqFile, BarcodesIndex &BarcodesIndex, string barcodesList, unsigned nbThreads=1)
vector< string >	retrieveReadsWithBarcodeBits_Gzip_Stream_Index (FILE *in, struct access *gzIndex, BarcodesIndex &barcodexIndex, barcode bc)
vector< string >	retrieveReadsWithBarcodeBits_Gzip (string fastqFile, BarcodesIndex &barcodexIndex, barcode bc)
vector< string >	retrieveReadsWithBarcode_Gzip_Stream_Index (FILE *in, struct access *gzIndex, BarcodesIndex &BarcodesIndex, string barcode)
vector< string >	retrieveReadsWithBarcode_Gzip (string fastqFile, BarcodesIndex &BarcodesIndex, string barcode)
vector< string >	retrieveReadsWithBarcodes_Gzip_Stream_Index (FILE *in, struct access *gzIndex, BarcodesIndex &BarcodesIndex, string barcodesList)
vector< string >	retrieveReadsWithBarcodes_Gzip (string fastqFile, BarcodesIndex &BarcodesIndex, string barcodesList, unsigned nbThreads=1)

Function Documentation

retrieveReadsWithBarcode()

vector<string> retrieveReadsWithBarcode	(	string	fastqFile,
		BarcodesIndex &	BarcodesIndex,
		string	bc
	)

Retrieve all the reads that share a given barcode, in a given fastq file.

Parameters

fastqFile	fastq file to extract reads from
BarcodesIndex	barcode index of the fastq file
bc	barcode of interest

Returns

a vector containing all the reads with the barcode of interest

retrieveReadsWithBarcode_Gzip()

vector<string> retrieveReadsWithBarcode_Gzip	(	string	fastqFile,
		BarcodesIndex &	BarcodesIndex,
		string	barcode
	)

Retrieve all the reads that share a given barcode, in a given gzipped fastq file, using its index.

Parameters

fastqFile	gzipped fastq file to extract reads from
BarcodesIndex	barcode index of the fastq file
bc	barcode of interest

Returns

a vector containing all the reads with the barcode of interest

retrieveReadsWithBarcode_Gzip_Stream_Index()

vector<string> retrieveReadsWithBarcode_Gzip_Stream_Index	(	FILE *	in,
		struct access *	gzIndex,
		BarcodesIndex &	BarcodesIndex,
		string	barcode
	)

Retrieve all the reads that share a given barcode, in a given gzipped fastq file, using its index.

Parameters

in	FILE open on the desired gzipped fastq file
gzIndex	index of the gzipped fastq file
BarcodesIndex	barcode index of the gzipped fastq file
bc	barcode of interest

Returns

a vector containing all the reads with the barcode of interest

retrieveReadsWithBarcode_Stream()

vector<string> retrieveReadsWithBarcode_Stream	(	ifstream &	reader,
		BarcodesIndex &	BarcodesIndex,
		string	bc
	)

Retrieve all the reads that share a given barcode, in a given fastq file.

Parameters

in	stream open on the desired fastq file
BarcodesIndex	barcode index of the fastq file
bc	barcode of interest

Returns

a vector containing all the reads with the barcode of interest

retrieveReadsWithBarcodeBits()

vector<string> retrieveReadsWithBarcodeBits	(	string	fastqFile,
		BarcodesIndex &	BarcodesIndex,
		barcode	bc
	)

Retrieve all the reads that share a given barcode, in a given fastq file.

Parameters

fastqFile	fastq file to extract reads from
BarcodesIndex	barcode index of the fastq file
bc	barcode of interest, in binary representation

Exceptions

ios_base::failure

thrown if fastqFile could not be open

Returns

a vector containing all the reads with the barcode of interest

retrieveReadsWithBarcodeBits_Gzip()

vector<string> retrieveReadsWithBarcodeBits_Gzip	(	string	fastqFile,
		BarcodesIndex &	barcodexIndex,
		barcode	bc
	)

Retrieve all the reads that share a given barcode, in a given gzipped fastq file, using its index.

Parameters

fastqFile	gzipped fastq file to extract reads from
BarcodesIndex	barcode index of the fastq file
bc	barcode of interest, in binary representation

Exceptions

ios_base::failure

thrown if fastqFile could not be open

Returns

a vector containing all the reads with the barcode of interest

retrieveReadsWithBarcodeBits_Gzip_Stream_Index()

vector<string> retrieveReadsWithBarcodeBits_Gzip_Stream_Index	(	FILE *	in,
		struct access *	gzIndex,
		BarcodesIndex &	barcodexIndex,
		barcode	bc
	)

Retrieve all the reads that share a given barcode, in a given gzipped fastq file, using its index.

Parameters

in	FILE open on the desired gzipped fastq file
gzIndex	index of the gzipped fastq file
BarcodesIndex	barcode index of the gzipped fastq file
bc	barcode of interest, in binary representation

Returns

a vector containing all the reads with the barcode of interest

retrieveReadsWithBarcodeBits_Stream()

vector<string> retrieveReadsWithBarcodeBits_Stream	(	ifstream &	in,
		BarcodesIndex &	BarcodesIndex,
		barcode	bc
	)

Retrieve all the reads that share a given barcode, in a given fastq file.

Parameters

in	stream open on the desired fastq file
BarcodesIndex	barcode index of the fastq file
bc	barcode of interest, in binary representation

Exceptions

runtime_error

thrown if a given offset of the file where the barcode appears could not be seeked

Returns

a vector containing all the reads with the barcode of interest

retrieveReadsWithBarcodes()

vector<string> retrieveReadsWithBarcodes	(	string	fastqFile,
		BarcodesIndex &	BarcodesIndex,
		string	barcodesList,
		unsigned	nbThreads = 1
	)

Retrieve all the reads of a fastq file that share a barcode appearing in the list of a given file

Parameters

fastqFile	fastq file to extract reads from
BarcodesIndex	barcode index of the fastq file
barcodesList	file containing the list of barcodes of interest, with one barcode per line
nbThreads	number of threads to use, set to 1 by default

Exceptions

ios_base::failure

thrown if fastqFile or barcodesList could not be open

Returns

a vector containing all the reads with the barcodes of interest

retrieveReadsWithBarcodes_Gzip()

vector<string> retrieveReadsWithBarcodes_Gzip	(	string	fastqFile,
		BarcodesIndex &	BarcodesIndex,
		string	barcodesList,
		unsigned	nbThreads = 1
	)

Retrieve all the reads of a fastq file that share a barcode appearing in the list of a given file

Parameters

fastqFile	fastq file to extract reads from
BarcodesIndex	barcode index of the fastq file
barcodesList	file containing the list of barcodes of interest, with one barcode per line
nbThreads	number of threads to use, set to 1 by default

Exceptions

ios_base::failure

thrown if fastqFile or barcodesList could not be open

Returns

a vector containing all the reads with the barcodes of interest

retrieveReadsWithBarcodes_Gzip_Stream_Index()

vector<string> retrieveReadsWithBarcodes_Gzip_Stream_Index	(	FILE *	in,
		struct access *	gzIndex,
		BarcodesIndex &	BarcodesIndex,
		string	barcodesList
	)

Retrieve all the reads of a gzipped fastq file that share a barcode appearing in the list of a given file

Parameters

in	FILE open on the desired gzipped fastq file
gzIndex	index of the gzipped fastq file
BarcodesIndex	barcode index of the fastq file
barcodesList	file containing the list of barcodes of interest, with one barcode per line

Exceptions

ios_base::failure

thrown if barcodesList could not be open

Returns

a vector containing all the reads with the barcodes of interest

retrieveReadsWithBarcodes_Stream()

vector<string> retrieveReadsWithBarcodes_Stream	(	ifstream &	in,
		BarcodesIndex &	BarcodesIndex,
		string	barcodesList
	)

Retrieve all the reads of a fastq file that share a barcode appearing in the list of a given file

Parameters

in	stream open on the desired fastq file
BarcodesIndex	barcode index of the fastq file
barcodesList	file containing the list of barcodes of interest, with one barcode per line

Exceptions

ios_base::failure

thrown if barcodesList could not be open

Returns

a vector containing all the reads with the barcodes of interest