Classes | Public Types | Public Member Functions | Public Attributes
ReferenceGenome Class Reference

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

#include <refgenome.hh>

List of all members.


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

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< MatchDescriptorgetAllReadPosBoth (FastQRead *fq)
dnapos_t getReadPosBoth (FastQRead *fq, int qlimit)
vector< dnapos_tgetReadPositions (const std::string &nucleotides)
vector< dnapos_tgetGCHisto ()
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< GenomeLocusMappingd_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< Unmatchedd_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 > 
string d_name

Detailed Description

Represents a reference genome to be aligned against.

Member Typedef Documentation

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 
string ReferenceGenome::getMatchingFastQs ( dnapos_t  start,
dnapos_t  stop,
StereoFASTQReader fastq 
vector<uint32_t> ReferenceGenome::getMatchingHashes ( const vector< uint32_t > &  hashes)
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

Member Data Documentation

vector<unsigned int> ReferenceGenome::d_correctMappings
vector<unsigned int> ReferenceGenome::d_gcMappings
unordered_map<dnapos_t, unsigned int> ReferenceGenome::d_insertCounts
vector<vector<uint32_t> > ReferenceGenome::d_kmerMappings
vector<unsigned int> ReferenceGenome::d_taMappings
vector<unsigned int> ReferenceGenome::d_wrongMappings

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