bpp-seq
2.2.0
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The poly sequence file format from phred software. More...
#include <Bpp/Seq/Io/PhredPoly.h>
Public Member Functions | |
PhredPoly (double ratio=0.8) | |
Build a new PhredPoly object. More... | |
virtual | ~PhredPoly () |
The AbstractISequence interface. | |
bool | nextSequence (std::istream &input, Sequence &seq) const throw (Exception) |
Read sequence from stream. More... | |
The IOSequence interface. | |
const std::string | getDataType () const |
const std::string | getFormatName () const |
const std::string | getFormatDescription () const |
Protected Attributes | |
double | ratio_ |
The poly sequence file format from phred software.
This class read DNA sequence from poly files produced by the phred program from the University of Washington. For now, only read raw sequences and do a basic filter on heterozygous site.
Definition at line 55 of file PhredPoly.h.
PhredPoly::PhredPoly | ( | double | ratio = 0.8 | ) |
Build a new PhredPoly object.
Definition at line 50 of file PhredPoly.cpp.
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inlinevirtual |
Definition at line 66 of file PhredPoly.h.
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inline |
Definition at line 82 of file PhredPoly.h.
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inline |
Definition at line 84 of file PhredPoly.h.
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inline |
Definition at line 83 of file PhredPoly.h.
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virtual |
Read sequence from stream.
Read one sequence from a stream.
input | The stream to read. |
seq | The sequence to fill. |
Exception | IOExecption and Sequence related Exceptions. |
Implements bpp::ISequenceStream.
Definition at line 54 of file PhredPoly.cpp.
References bpp::Alphabet::getGeneric().
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protected |
Definition at line 57 of file PhredPoly.h.