eXpress “1.5”
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The BAMParser class fills Fragment objects by parsing an input file in BAM format. More...
#include <mapparser.h>
Public Member Functions | |
BAMParser (BamTools::BamReader *reader) | |
BAMParser constructor sets the reader. | |
const std::string | header () const |
An accessor for the header string. | |
bool | next_fragment (Fragment &f) |
A member function that loads all mappings of the next fragment into the given Fragment object. | |
void | reset () |
A member function that resets the parser and rewinds to the beginning of the BAM file. |
The BAMParser class fills Fragment objects by parsing an input file in BAM format.
Definition at line 127 of file mapparser.h.
BAMParser::BAMParser | ( | BamTools::BamReader * | reader | ) |
BAMParser constructor sets the reader.
reader | a pointer to the BamReader object that will directly parse the BAM file. |
Definition at line 239 of file mapparser.cpp.
const std::string BAMParser::header | ( | ) | const [inline, virtual] |
An accessor for the header string.
Implements Parser.
Definition at line 152 of file mapparser.h.
bool BAMParser::next_fragment | ( | Fragment & | f | ) | [virtual] |
A member function that loads all mappings of the next fragment into the given Fragment object.
f | the empty Fragment to add mappings to. |
Implements Parser.
Definition at line 261 of file mapparser.cpp.