Parser for text files with repertoire data. By default it's MiTCR parser. To make new parsers inherit from this class and rewrite virtual private method "parseRepertoire". More...

#include <parser.h>

Public Types
typedef Json::Value	ParserConfig
	Parameters of this parser: parser's name, names of the columns, separators, sequences and other.

Public Member Functions
bool	open (const std::string &filepath, const VDJRecombinationGenes &gene_segments, SequenceType seq_type, Recombination recomb, AlignmentColumnOptions opts=AlignmentColumnOptions().setV(AlignmentColumnOptions::USE_PROVIDED).setJ(AlignmentColumnOptions::USE_PROVIDED).setD(AlignmentColumnOptions::OVERWRITE), VDJAlignerParameters params=VDJAlignerParameters())
	Parse text file with sequence alignment data and return constructed Cloneset. More...

bool	parse (Cloneset *cloneset, size_t max_clonotype_count=(size_t)-1)

bool	openAndParse (const std::string &filepath, Cloneset *cloneset, const VDJRecombinationGenes &gene_segments, SequenceType seq_type, Recombination recomb, AlignmentColumnOptions opts=AlignmentColumnOptions().setV(AlignmentColumnOptions::USE_PROVIDED).setJ(AlignmentColumnOptions::USE_PROVIDED).setD(AlignmentColumnOptions::OVERWRITE), VDJAlignerParameters params=VDJAlignerParameters())

Protected Member Functions
void	parseRepertoire (ClonotypeVector &vec, size_t max_clonotype_count)

template<GeneSegments GENE>
void	parseSegment (stringstream &symbol_stream, const string &segment_word, vector< seg_index_t > &segvec, const GeneSegmentAlphabet &gsa, size_t line_num, char segment_sep, string &temp_str)

void	parseAlignment (stringstream &symbol_stream, const string &segment_word, const vector< seg_index_t > &segvec, GeneSegments gene, const GeneSegmentAlphabet &gsa, size_t line_num, char segment_sep, char internal_sep, string &temp_str, stringstream &temp_stream)

std::string	get_prefix (const string &filename) const

Protected Attributes
std::ifstream	_stream

VDJRecombinationGenes	_genes

Recombination	_recomb

AlignmentColumnOptions	_opts

SequenceType	_seq_type

RepertoireParserStatistics	_stats

Aligner	_aligner

bool	_status

bool	_read_header

Detailed Description

template<typename Aligner>
class ymir::RepertoireParser< Aligner >

Parser for text files with repertoire data. By default it's MiTCR parser. To make new parsers inherit from this class and rewrite virtual private method "parseRepertoire".

Member Function Documentation

template<typename Aligner >

bool ymir::RepertoireParser< Aligner >::open	(	const std::string &	filepath,
		const VDJRecombinationGenes &	gene_segments,
		SequenceType	seq_type,
		Recombination	recomb,
		AlignmentColumnOptions	opts = `AlignmentColumnOptions().setV(AlignmentColumnOptions::USE_PROVIDED).setJ(AlignmentColumnOptions::USE_PROVIDED).setD(AlignmentColumnOptions::OVERWRITE)`,
		VDJAlignerParameters	params = `VDJAlignerParameters()`
	)

inline

Parse text file with sequence alignment data and return constructed Cloneset.

Parse all lines in the file and return a repertoire. If no alignments found or any of align_* parameters is true, create alignment using input aligner from function loadFile().

Parameters

filepath	Path to a file with sequences.
gene_segments	Alphabets of gene segments.
seq_type
recomb
opts	What action to do with columns with V, D and J alignments.

Returns: True if found has been successfully processed, false otherwise.

template<typename Aligner >

bool ymir::RepertoireParser< Aligner >::parse	(	Cloneset *	cloneset,
		size_t	max_clonotype_count = `(size_t)-1`
	)

inline

Parameters

cloneset Pointer to clonal repertoire object to which data will be uploaded.

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

Ymir/src/parser.h

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

template<typename Aligner> class ymir::RepertoireParser< Aligner >

Member Function Documentation

template<typename Aligner>
class ymir::RepertoireParser< Aligner >