barcodesComparison.h File Reference

#include "utils.h"
#include "indexManagementBam.h"

Include dependency graph for barcodesComparison.h:

Go to the source code of this file.

Classes
struct	hashPairs

Functions
unsigned	countCommonBarcodes (robin_hood::unordered_set< barcode > barcodes1, robin_hood::unordered_set< barcode > barcodes2)
robin_hood::unordered_map< pair< string, string >, unsigned, hashPairs >	computePairwiseCommonBarcounts (robin_hood::unordered_map< string, robin_hood::unordered_set< barcode >> regionsBarcodes)
robin_hood::unordered_map< pair< string, string >, unsigned, hashPairs >	compareRegions (string bamFile, string regions)
void	computeCommonBarcodesCounts (robin_hood::unordered_map< pair< string, string >, unsigned, hashPairs > &counts, BarcodesOffsetsIndex &BarcodesOffsetsIndex, BamReader &reader, const RefVector &rv, int size, string &qRegion)
robin_hood::unordered_map< pair< string, string >, unsigned, hashPairs >	compareContig_BamReader (string bamFile, BarcodesOffsetsIndex &BarcodesOffsetsIndex, string contig, int size)
robin_hood::unordered_map< pair< string, string >, unsigned, hashPairs >	compareContig (string bamFile, BarcodesOffsetsIndex &BarcodesOffsetsIndex, string contig, int size)
robin_hood::unordered_map< pair< string, string >, unsigned, hashPairs >	compareContigs (string bamFile, BarcodesOffsetsIndex &BarcodesOffsetsIndex, string contigs, int size, unsigned nbThreads=1)

Function Documentation

compareContig()

robin_hood::unordered_map<pair<string, string>, unsigned, hashPairs> compareContig	(	string	bamFile,
		BarcodesOffsetsIndex &	BarcodesOffsetsIndex,
		string	contig,
		int	size
	)

Compare the barcodes of a given contig's extremities to the barcodes of other contigs' extremities.

Parameters

bamFile	BAM file to compare contigs' extremities barcodes from
BarcodesOffsetsIndex	barcode index associating barcodes to the set of BamRegion they appear in
contig	name of the contig of interest
size	size of the contigs extremities to consider

Exceptions

ios_base::failure

thrown if bamFile or its associated index could not be open,

Returns

a map associating pairs of contigs' extremities to their number of common barcodes

compareContig_BamReader()

robin_hood::unordered_map<pair<string, string>, unsigned, hashPairs> compareContig_BamReader	(	string	bamFile,
		BarcodesOffsetsIndex &	BarcodesOffsetsIndex,
		string	contig,
		int	size
	)

Compare the barcodes of a given contig's extremities to the barcodes of other contigs' extremities.

Parameters

reader	BamReader open on the desired BAM file
BarcodesOffsetsIndex	barcode index associating barcodes to the set of BamRegion they appear in
contig	name of the contig of interest
size	size of the contigs extremities to consider

Exceptions

runtime_error

is trown if the ID of contig could not be found

Returns

a map associating pairs of contigs' extremities to their number of common barcodes

compareContigs()

robin_hood::unordered_map<pair<string, string>, unsigned, hashPairs> compareContigs	(	string	bamFile,
		BarcodesOffsetsIndex &	BarcodesOffsetsIndex,
		string	contigs,
		int	size,
		unsigned	nbThreads = 1
	)

Compare the barcodes of a given list of contigs' extremities to the barcodes of other contigs' extremities.

Parameters

bamFile	BAM file to compare contigs' extremities barcodes from
BarcodesOffsetsIndex	barcode index associating barcodes to the set of BamRegion they appear in
contigs	file containing a list of contigs of interest
size	size of the contigs extremities to consider
nbThreads	number of threads to use, set to 1 by default

Exceptions

ios_base::failure

thrown if bamFile or its associated index, or if regions could not be open

Returns

a map associating pairs of contigs' extremities to their number of common barcodes

compareRegions()

robin_hood::unordered_map<pair<string, string>, unsigned, hashPairs> compareRegions	(	string	bamFile,
		string	regions
	)

Compute the number of barcodes that are shared between all possible pair of regions contained in a file.

Parameters

reader	bamFile BAM file to compute common barcodes from
regions	file containing a list of regions formatted as chromosome:startPosition-endPosition

Exceptions

ios_base::failure

thrown if bamFile or its associated index, or if regions could not be open

Returns

a map associating all possible pairs of regions to their number of common barcodes

computeCommonBarcodesCounts()

void computeCommonBarcodesCounts	(	robin_hood::unordered_map< pair< string, string >, unsigned, hashPairs > &	counts,
		BarcodesOffsetsIndex &	BarcodesOffsetsIndex,
		BamReader &	reader,
		const RefVector &	rv,
		int	size,
		string &	qRegion
	)

Compute the number of barcodes that are shared between a given contig's extremity and other contigs' extremities.

Parameters

counts	map associating pairs of contigs' extremities to their number of common barcodes
BarcodesOffsetsIndex	barcode index associating barcodes to the set of BamRegion they appear in
reader	BamReader open on the desired BAM file
rv	vector containing the information (name and length) about reference sequences
size	size of the contigs extremities to consider
qRegion	region of the contig extremity of interest

computePairwiseCommonBarcounts()

robin_hood::unordered_map<pair<string, string>, unsigned, hashPairs> computePairwiseCommonBarcounts

(

robin_hood::unordered_map< string, robin_hood::unordered_set< barcode >>

regionsBarcodes

)

Compute the number of barcodes that are shared between all possible pair of regions contained in a map.

Parameters

regionsBarcodes

map associating every region of interest to its set of barcodes

Returns

a map associating all possible pairs of regions to their number of common barcodes

countCommonBarcodes()

unsigned countCommonBarcodes	(	robin_hood::unordered_set< barcode >	barcodes1,
		robin_hood::unordered_set< barcode >	barcodes2
	)

Count the number of common barcodes between two sets of barcodes.

Parameters

barcodes1	first set of barcodes
barcodes2	second set of barcodes

Returns

the number of common barcodes between the two sets