ReferenceGenome Class Reference

Represents a reference genome to be aligned against. More...

#include <refgenome.hh>

List of all members.

Classes
struct	HashPos
struct	LociStats
	statistics for a locus More...
struct	MatchDescriptor
	Describes how a FastQRead (not mentioned) matches to the reference (straight or in reverse), and what the matching score is. More...
Public Types
typedef unordered_map < dnapos_t, LociStats >	locimap_t
Public Member Functions
	ReferenceGenome (const string &fname)
	Read reference from FASTA.
dnapos_t	size () const
vector< uint32_t >	getMatchingHashes (const vector< uint32_t > &hashes)
void	mapFastQ (dnapos_t pos, const FastQRead &fqfrag, int indel=0)
void	cover (dnapos_t pos, char quality, int limit)
void	cover (dnapos_t pos, unsigned int length, const std::string &quality, int limit)
vector< MatchDescriptor >	getAllReadPosBoth (FastQRead *fq)
dnapos_t	getReadPosBoth (FastQRead *fq, int qlimit)
vector< dnapos_t >	getReadPositions (const std::string &nucleotides)
vector< dnapos_t >	getGCHisto ()
string	snippet (dnapos_t start, dnapos_t stop) const
void	printCoverage (FILE *jsfp, const std::string &fname)
void	index (unsigned int length)
string	getMatchingFastQs (dnapos_t pos, StereoFASTQReader &fastq)
string	getMatchingFastQs (dnapos_t start, dnapos_t stop, StereoFASTQReader &fastq)
Public Attributes
vector< GenomeLocusMapping >	d_mapping
vector< unsigned int >	d_correctMappings
vector< unsigned int >	d_wrongMappings
vector< unsigned int >	d_gcMappings
vector< unsigned int >	d_taMappings
vector< vector< uint32_t > >	d_kmerMappings
vector< Unmatched >	d_unmRegions
dnapos_t	d_aCount
dnapos_t	d_cCount
dnapos_t	d_gCount
dnapos_t	d_tCount
locimap_t	d_locimap
unordered_map< dnapos_t, unsigned int >	d_insertCounts
string	d_name

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Detailed Description

Represents a reference genome to be aligned against.

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Member Typedef Documentation

typedef unordered_map<dnapos_t, LociStats> ReferenceGenome::locimap_t

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Constructor & Destructor Documentation

ReferenceGenome::ReferenceGenome

(

const string &

fname

)

Read reference from FASTA.

---

Member Function Documentation

void ReferenceGenome::cover	(	dnapos_t	pos,
		char	quality,
		int	limit
	)

void ReferenceGenome::cover	(	dnapos_t	pos,
		unsigned int	length,
		const std::string &	quality,
		int	limit
	)

vector< ReferenceGenome::MatchDescriptor > ReferenceGenome::getAllReadPosBoth

(

FastQRead *

fq

)

vector< dnapos_t > ReferenceGenome::getGCHisto

(

)

string ReferenceGenome::getMatchingFastQs	(	dnapos_t	pos,
		StereoFASTQReader &	fastq
	)

string ReferenceGenome::getMatchingFastQs	(	dnapos_t	start,
		dnapos_t	stop,
		StereoFASTQReader &	fastq
	)

vector<uint32_t> ReferenceGenome::getMatchingHashes

(

const vector< uint32_t > &

hashes

)

dnapos_t ReferenceGenome::getReadPosBoth	(	FastQRead *	fq,
		int	qlimit
	)

vector< dnapos_t > ReferenceGenome::getReadPositions

(

const std::string &

nucleotides

)

void ReferenceGenome::index

(

unsigned int

length

)

void ReferenceGenome::mapFastQ	(	dnapos_t	pos,
		const FastQRead &	fqfrag,
		int	indel = 0
	)

void ReferenceGenome::printCoverage	(	FILE *	jsfp,
		const std::string &	fname
	)

dnapos_t ReferenceGenome::size

(

)

const [inline]

string ReferenceGenome::snippet	(	dnapos_t	start,
		dnapos_t	stop
	)		const

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Member Data Documentation

dnapos_t ReferenceGenome::d_aCount

dnapos_t ReferenceGenome::d_cCount

vector<unsigned int> ReferenceGenome::d_correctMappings

vector<unsigned int> ReferenceGenome::d_gcMappings

dnapos_t ReferenceGenome::d_gCount

unordered_map<dnapos_t, unsigned int> ReferenceGenome::d_insertCounts

vector<vector<uint32_t> > ReferenceGenome::d_kmerMappings

locimap_t ReferenceGenome::d_locimap

vector<GenomeLocusMapping> ReferenceGenome::d_mapping

string ReferenceGenome::d_name

vector<unsigned int> ReferenceGenome::d_taMappings

dnapos_t ReferenceGenome::d_tCount

vector<Unmatched> ReferenceGenome::d_unmRegions

vector<unsigned int> ReferenceGenome::d_wrongMappings

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

• refgenome.hh
• antonie.cc
• refgenome.cc