antonie.cc File Reference

#include <tclap/CmdLine.h>
#include <stdio.h>
#include <stdint.h>
#include <fstream>
#include <map>
#include <unordered_map>
#include <string.h>
#include <stdexcept>
#include <forward_list>
#include <inttypes.h>
#include <numeric>
#include <unistd.h>
#include <errno.h>
#include <math.h>
#include <boost/progress.hpp>
#include <boost/format.hpp>
#include <boost/iostreams/tee.hpp>
#include <boost/iostreams/stream.hpp>
#include <boost/algorithm/string.hpp>
#include <boost/lexical_cast.hpp>
#include "dnamisc.hh"
#include <fenv.h>
#include "geneannotated.hh"
#include "misc.hh"
#include "fastq.hh"
#include <mba/diff.h>
#include <mba/msgno.h>
#include "antonie.hh"
#include "saminfra.hh"
#include "refgenome.hh"
#include "hash.h"

Classes
class	DuplicateCounter
	Very simple duplicate count estimator using a simple hash. Also provides statistics. More...
struct	qtally
	Keeps a tally of correct and incorrect mappings. More...
Defines
#define	__STDC_FORMAT_MACROS
Typedefs
typedef io::tee_device < std::ostream, std::ostringstream >	TeeDevice
typedef io::stream< TeeDevice >	TeeStream
typedef vector< VarMeanEstimator >	qstats_t
Functions
int	MBADiff (dnapos_t pos, const FastQRead &fqr, const string &reference)
	0 if nothing interesting, positive if our read has insert at that position, negative if we have a delete at that position
unsigned int	diffScore (ReferenceGenome &rg, dnapos_t pos, FastQRead &fqfrag, int qlimit)
vector< dnapos_t >	getTriplets (const vector< pair< dnapos_t, char >> &together, unsigned int interval, unsigned int shift)
void	printCorrectMappings (FILE *jsfp, const ReferenceGenome &rg, const std::string &name)
void	printGCMappings (FILE *jsfp, const ReferenceGenome &rg, const std::string &name)
int	MapToReference (ReferenceGenome &rg, dnapos_t pos, FastQRead fqfrag, int qlimit, SAMWriter *sw, vector< qtally > *qqcounts, int *outIndel=0)
void	emitRegion (FILE *fp, ReferenceGenome &rg, StereoFASTQReader &fastq, GeneAnnotationReader &gar, const string &name, unsigned int index, dnapos_t start, dnapos_t stop, const std::string &report_="")
void	emitRegion (FILE *fp, ReferenceGenome &rg, StereoFASTQReader &fastq, GeneAnnotationReader &gar, const string &name, unsigned int index, dnapos_t start, const std::string &report="")
unsigned int	variabilityCount (const ReferenceGenome &rg, dnapos_t position, const ReferenceGenome::LociStats &lc, double *fraction)
vector < ReferenceGenome::MatchDescriptor >	fuzzyFind (FastQRead *fqfrag, ReferenceGenome &rg, int keylen, int qlimit)
void	writeUnmatchedReads (const vector< uint64_t > &unfoundReads, StereoFASTQReader &fastq)
void	printQualities (FILE *jsfp, const qstats_t &qstats)
int	main (int argc, char **argv)
Variables
TeeStream *	g_log

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Define Documentation

#define __STDC_FORMAT_MACROS

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Typedef Documentation

typedef vector<VarMeanEstimator> qstats_t

typedef io::tee_device<std::ostream, std::ostringstream> TeeDevice

typedef io::stream< TeeDevice > TeeStream

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Function Documentation

unsigned int diffScore	(	ReferenceGenome &	rg,
		dnapos_t	pos,
		FastQRead &	fqfrag,
		int	qlimit
	)

void emitRegion	(	FILE *	fp,
		ReferenceGenome &	rg,
		StereoFASTQReader &	fastq,
		GeneAnnotationReader &	gar,
		const string &	name,
		unsigned int	index,
		dnapos_t	start,
		dnapos_t	stop,
		const std::string &	report_ = ""
	)

void emitRegion	(	FILE *	fp,
		ReferenceGenome &	rg,
		StereoFASTQReader &	fastq,
		GeneAnnotationReader &	gar,
		const string &	name,
		unsigned int	index,
		dnapos_t	start,
		const std::string &	report = ""
	)

vector<ReferenceGenome::MatchDescriptor> fuzzyFind	(	FastQRead *	fqfrag,
		ReferenceGenome &	rg,
		int	keylen,
		int	qlimit
	)

vector<dnapos_t> getTriplets	(	const vector< pair< dnapos_t, char >> &	together,
		unsigned int	interval,
		unsigned int	shift
	)

int main	(	int	argc,
		char **	argv
	)

int MapToReference	(	ReferenceGenome &	rg,
		dnapos_t	pos,
		FastQRead	fqfrag,
		int	qlimit,
		SAMWriter *	sw,
		vector< qtally > *	qqcounts,
		int *	outIndel = 0
	)

int MBADiff	(	dnapos_t	pos,
		const FastQRead &	fqr,
		const string &	reference
	)

0 if nothing interesting, positive if our read has insert at that position, negative if we have a delete at that position

void printCorrectMappings	(	FILE *	jsfp,
		const ReferenceGenome &	rg,
		const std::string &	name
	)

void printGCMappings	(	FILE *	jsfp,
		const ReferenceGenome &	rg,
		const std::string &	name
	)

void printQualities	(	FILE *	jsfp,
		const qstats_t &	qstats
	)

unsigned int variabilityCount	(	const ReferenceGenome &	rg,
		dnapos_t	position,
		const ReferenceGenome::LociStats &	lc,
		double *	fraction
	)

void writeUnmatchedReads	(	const vector< uint64_t > &	unfoundReads,
		StereoFASTQReader &	fastq
	)

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Variable Documentation

TeeStream* g_log