Definition at line 6 of file Chromosome.h.
◆ Chromosome() [1/4]
Chromosome::Chromosome |
( |
GenomeSequence * |
gs, |
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unsigned int |
chrosomeIndex |
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) |
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explicit |
Definition at line 4 of file Chromosome.cpp.
5{
6 assert(gs);
8
9 this->gs = gs;
10 this->chromosomeIndex = chromosomeIndex;
13}
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
genomeIndex_t getChromosomeSize(int chromosomeIndex) const
given a chromosome, return its size in bases
◆ Chromosome() [2/4]
Chromosome::Chromosome |
( |
GenomeSequence * |
gs, |
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const char * |
chromosomeName |
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) |
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explicit |
Definition at line 15 of file Chromosome.cpp.
16{
17 assert(gs);
18 this->gs = gs;
19
21 assert(chromosomeIndex != INVALID_CHROMOSOME_INDEX);
22
25}
int getChromosome(genomeIndex_t position) const
given a whole genome index, get the chromosome it is located in
◆ Chromosome() [3/4]
Chromosome::Chromosome |
( |
const char * |
genomseSequenceFileName, |
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unsigned int |
chromosomeIndex, |
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bool |
isColorSpace |
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) |
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explicit |
Definition at line 27 of file Chromosome.cpp.
28{
29 std::string s(genomseSequenceFileName);
31 assert(gs);
33 assert(!gs->
open(isColorSpace));
34 this->chromosomeIndex = chromosomeIndex;
37}
Create/Access/Modify/Load Genome Sequences stored as binary mapped files.
bool setReferenceName(std::string referenceFilename)
set the reference name that will be used in open()
bool open(bool isColorSpace=false, int flags=O_RDONLY)
open the reference specified using GenomeSequence::setReferenceName
◆ Chromosome() [4/4]
Chromosome::Chromosome |
( |
const std::string & |
genomseSequenceFileName, |
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unsigned int |
chromosomeIndex, |
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bool |
isColorSpace |
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) |
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explicit |
Definition at line 39 of file Chromosome.cpp.
40{
42 assert(gs);
44 assert(!gs->
open(isColorSpace));
45 this->chromosomeIndex = chromosomeIndex;
48}
◆ Length()
genomeIndex_t Chromosome::Length |
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| ) |
const |
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inline |
Definition at line 12 of file Chromosome.h.
13 {
14 return chromosomeSize;
15 }
◆ Name()
const char * Chromosome::Name |
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const |
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inline |
Definition at line 22 of file Chromosome.h.
22 {
23 return gs->getChromosomeName(this->chromosomeIndex);
24 }
◆ operator[]()
char Chromosome::operator[] |
( |
genomeIndex_t |
index | ) |
const |
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inline |
Definition at line 17 of file Chromosome.h.
18 {
19 index += offset;
20 return (*gs)[index];
21 }
The documentation for this class was generated from the following files: