airr.cu File Reference

A collection of patching functions that add airr-format compatibility to cli.cu. More...

#include <stdio.h>
#include <string.h>
#include "codec.cu"

Functions
int	split_offset (char *str, int *&offsetOutput, int nColumn)
	private function More...
int	find_idx (char *haystack, const char *needle, int *offsets, int offsetLen)
	private function More...
int	find_header (char *line, int &cdrIndexOut, int &freqIndexOut, bool doubleCol)
	private function More...
int	extract_data (char *line, int cdrIndex, int freqIndex, int nColumn, int lineNumber, SeqArray *seqOut, int &freqOut, bool doubleCol)
	private function More...
int	parse_airr_input (char *path, SeqArray *seqOut, SeqInfo *freqOut, int len, bool doubleCol)
	read and parse input airr file to SeqArray and maybe SeqInfo More...

Variables
const int	DEFAULT_MAX_COLUMN = 300
	maximum number of tsv columns More...
const int	DEFAULT_LINE_SIZE = 5000
	maximum number of characters in a line More...
const char	DELIMITER = '\t'
	tsv delimitter More...
const char	CDR_FIELD [8] = "cdr3_aa"
	field header for sequence data More...
const char	FREQ_FIELD [16] = "duplicate_count"
	field header for sequence data More...

Detailed Description

A collection of patching functions that add airr-format compatibility to cli.cu.

Function Documentation

extract_data()

int extract_data	(	char *	line,
		int	cdrIndex,
		int	freqIndex,
		int	nColumn,
		int	lineNumber,
		SeqArray *	seqOut,
		int &	freqOut,
		bool	doubleCol
	)

private function

find_header()

int find_header	(	char *	line,
		int &	cdrIndexOut,
		int &	freqIndexOut,
		bool	doubleCol
	)

private function

find_idx()

int find_idx	(	char *	haystack,
		const char *	needle,
		int *	offsets,
		int	offsetLen
	)

private function

parse_airr_input()

int parse_airr_input	(	char *	path,
		SeqArray *	seqOut,
		SeqInfo *	freqOut,
		int	len,
		bool	doubleCol
	)

read and parse input airr file to SeqArray and maybe SeqInfo

Parameters

path	file path to read
seqOut	output sequences
freqOut	output frequency, if doubleCol is set to true
len	expected length
doubleCol	if true, read freqOut

Returns

execution result

split_offset()

int split_offset	(	char *	str,
		int *&	offsetOutput,
		int	nColumn
	)

private function

Variable Documentation

CDR_FIELD

const char CDR_FIELD[8] = "cdr3_aa"

field header for sequence data

DEFAULT_LINE_SIZE

const int DEFAULT_LINE_SIZE = 5000

maximum number of characters in a line

DEFAULT_MAX_COLUMN

const int DEFAULT_MAX_COLUMN = 300

maximum number of tsv columns

DELIMITER

const char DELIMITER = '\t'

tsv delimitter

FREQ_FIELD

const char FREQ_FIELD[16] = "duplicate_count"

field header for sequence data