The fastq sequence file format.
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#include <Bpp/Seq/Io/Fastq.h>
The fastq sequence file format.
- Author
- Sylvain Gaillard
Definition at line 56 of file Fastq.h.
◆ Fastq()
bpp::Fastq::Fastq |
( |
bool |
repName = false | ) |
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inline |
Build a new Fastq object.
- Parameters
-
repName | Tell if the names in the file is repeated (tested on input) or must be repeated (for output). |
Definition at line 70 of file Fastq.h.
◆ ~Fastq()
virtual bpp::Fastq::~Fastq |
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| ) |
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inlinevirtual |
◆ getDataType()
const std::string bpp::Fastq::getDataType |
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| ) |
const |
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inline |
◆ getFormatDescription()
const std::string bpp::Fastq::getFormatDescription |
( |
| ) |
const |
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inline |
◆ getFormatName()
const std::string bpp::Fastq::getFormatName |
( |
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const |
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inline |
◆ nextSequence()
bool Fastq::nextSequence |
( |
std::istream & |
input, |
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Sequence & |
seq |
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) |
| const |
throw | ( | Exception |
| ) | | |
- Author
- Sylvain Gaillard
- Usage
DNA alpha;
SequenceWithQuality seq(&alpha);
std::ifstream in("reads.fastq");
while (fq.nextSequence(in, seq)) {
}
in.close();
Definition at line 47 of file Fastq.cpp.
◆ repeatName() [1/2]
bool bpp::Fastq::repeatName |
( |
| ) |
const |
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inline |
◆ repeatName() [2/2]
void bpp::Fastq::repeatName |
( |
bool |
yn | ) |
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inline |
◆ writeSequence()
void Fastq::writeSequence |
( |
std::ostream & |
output, |
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const Sequence & |
seq |
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) |
| const |
throw | ( | Exception |
| ) | | |
- Author
- Sylvain Gaillard
Definition at line 88 of file Fastq.cpp.
◆ repeatName_
bool bpp::Fastq::repeatName_ |
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private |
The documentation for this class was generated from the following files: