2 #include "Chromosome.h"
4 Chromosome::Chromosome(
GenomeSequence* gs,
unsigned int chromosomeIndex)
10 this->chromosomeIndex = chromosomeIndex;
15 Chromosome::Chromosome(
GenomeSequence* gs,
const char* chromosomeName)
21 assert(chromosomeIndex != INVALID_CHROMOSOME_INDEX);
27 Chromosome::Chromosome(
const char* genomseSequenceFileName,
unsigned int chromosomeIndex,
bool isColorSpace)
29 std::string s(genomseSequenceFileName);
33 assert(!gs->
open(isColorSpace));
34 this->chromosomeIndex = chromosomeIndex;
39 Chromosome::Chromosome(
const std::string& genomseSequenceFileName,
unsigned int chromosomeIndex,
bool isColorSpace)
44 assert(!gs->
open(isColorSpace));
45 this->chromosomeIndex = chromosomeIndex;
Create/Access/Modify/Load Genome Sequences stored as binary mapped files.
int getChromosomeCount() const
Return the number of chromosomes in the genome.
genomeIndex_t getChromosomeStart(int chromosomeIndex) const
given a chromosome, return the genome base it starts in
int getChromosome(genomeIndex_t position) const
given a whole genome index, get the chromosome it is located in
bool setReferenceName(std::string referenceFilename)
set the reference name that will be used in open()
genomeIndex_t getChromosomeSize(int chromosomeIndex) const
given a chromosome, return its size in bases
bool open(bool isColorSpace=false, int flags=O_RDONLY)
open the reference specified using GenomeSequence::setReferenceName