utils.h File Reference

#include <string>
#include <vector>
#include "api/BamReader.h"
#include "api/BamIndex.h"
#include "api/BamAux.h"
#include "robin_hood.h"
#include <sstream>
#include <regex>
#include "barcodesList.h"

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Macros
#define	BXTAG   "BX:Z"
#define	no_argument   0
#define	required_argument   1
#define	optional_argument   2

Typedefs
typedef vector< bool >	barcode

Enumerations
enum	SequencingTechnology {   Undefined = 0, TenX, Haplotagging, TELLSeq,   stLFR }

Functions
SequencingTechnology	determineSequencingTechnology (const string &barcode)
string	retrieveNucleotidesContent (const string &barcode)
bool	isValidBarcode (const string &barcode)
barcode	stringToBarcode (const string &str)
vector< string >	splitString (string s, string delimiter)
BamRegion	stringToBamRegion (BamReader &reader, string s)
vector< string >	extractRegions (string chromosome, int32_t chromosomeSize, unsigned regionSize)
vector< string >	extractRegionsList (BamReader &reader, unsigned regionSize)
string	convertToSam (const BamAlignment &a, RefVector m_references)

Variables
SequencingTechnology	techno

Macro Definition Documentation

BXTAG

#define BXTAG   "BX:Z"

Definition at line 14 of file utils.h.

no_argument

#define no_argument   0

Definition at line 16 of file utils.h.

optional_argument

#define optional_argument   2

Definition at line 18 of file utils.h.

required_argument

#define required_argument   1

Definition at line 17 of file utils.h.

Typedef Documentation

barcode

typedef vector<bool> barcode

Definition at line 23 of file utils.h.

Enumeration Type Documentation

SequencingTechnology

enum SequencingTechnology

Supported sequencing technologies

Enumerator
Undefined
TenX
Haplotagging
TELLSeq
stLFR

Definition at line 28 of file utils.h.

Function Documentation

convertToSam()

string convertToSam	(	const BamAlignment &	a,
		RefVector	m_references
	)

Translate a BamAlignment to a SAM-like string.

Parameters

a	BamAlignment to translate
m_references	vector containing the information (name and length) about reference sequences

Returns

a SAM-like string summarizing the information of a

determineSequencingTechnology()

SequencingTechnology determineSequencingTechnology

(

const string &

barcode

)

Determine the sequencing technology the barcode originates from. This function is compatible with 10x Genomics, Haplotagging, TELL-SEq and stLFR. Barcodes that do not come from these technologies and are not represented as a suite of nucleotides will cause the program to exit.

Parameters

barcode

the barcode to determine sequencing technology from

Exceptions

runtime_error

thrown if a barcode pattern could not be converted to a regexp or if the used sequencing technology was not recognized

Returns

The SequencingTechnology enum field corresponding to the sequencing technology

extractRegions()

vector<string> extractRegions	(	string	chromosome,
		int32_t	chromosomeSize,
		unsigned	regionSize
	)

Extract all regions of a given size from a civen chromosome.

Parameters

chromosme	chromosome of interest
chromosomeSize	size of the chromosome
regionSize	size of the regions to extract

Returns

a list of all regions of specifed size of the chromosome

extractRegionsList()

vector<string> extractRegionsList	(	BamReader &	reader,
		unsigned	regionSize
	)

Extract all regions from all chromosomes.

Parameters

reader	BamReader open on the desired BAM file
regionSize	size of the regions to extract

Exceptions

runtime_error

thrown if a contig name could not be converted to an ID or if a region of redaer could not be jumped to

Returns

a list of all regions of specified size of all the chromosomes

isValidBarcode()

bool isValidBarcode

(

const string &

barcode

)

Check whether a barcode is valid or not. A barcode is considered as valid if it is not empty, if it does not contain any "N" for 10x and TELL-Seq, if it is not "0_0_0" for stLFR data, and does not contain a "00" substring for Haplotagging data. The function takes care of determining the employed sequencing technoly.

Parameters

barcode

the barcode to verify

Exceptions

runtime_error

thrown if the sequencing technology could not be recognized

Returns

true if the barcode is valid, false otherwise

retrieveNucleotidesContent()

string retrieveNucleotidesContent

(

const string &

barcode

)

Retrieve the nucleotides content of the barcode. This function is used to translate barcodes represented as a suite of integers (as in stLFT and Haplotagging) into nucleotides barcodes. The function takes care of determining the employed sequencing technoly.

Parameters

barcode

the barcode to retrieve nucleotides for

Exceptions

runtime_error

thrown if the sequencing technology could not be recognized

Returns

the barcode in nucleotides representation

splitString()

vector<string> splitString	(	string	s,
		string	delimiter
	)

Split a string according to a delimiter.

Parameters

s	string to split
delimiter	delimiter

Returns

a vector containing the splits of the string

stringToBamRegion()

BamRegion stringToBamRegion	(	BamReader &	reader,
		string	s
	)

Translate a string to a BamRegion.

Parameters

reader	BamReader open on the desired BAM file
s	string to translate, formatted as chromosome:startPosition-endPosition

Exceptions

runtime_error

thrown if a region could not be converted to a BamRegion or if a contig name could not be converted to an ID

Returns

the BamRegion coressponding to the string s

stringToBarcode()

barcode stringToBarcode

(

const string &

str

)

Translate a string to a barcode in 2 bits per nucleotide format. The function takes care of determining the employed sequencing technoly, and of retrieving the nucleotides contents of barcodes represented as a suite of integers.

Parameters

str	string to convert

Returns

the barcode in binary representation

Variable Documentation

techno

SequencingTechnology techno