Provides support for manipulations on SAM/BAM and CGI Evidence CIGAR. More...
#include <SamRecord.hpp>
Classes | |
| class | CigarElement |
Public Types | |
| typedef std::vector< CigarElement > | ParsedCigar |
Public Member Functions | |
| Cigar (bool mergeNeighbours=false, bool removeZeros=false) | |
| Cigar (const std::string &cigar, bool mergeNeighbours=false, bool removeZeros=false) | |
| void | parse (const std::string &cigar) |
| size_t | getSequenceLength () const |
| computes length of the sequence the cigar describes | |
| size_t | getReferenceLength () const |
| computes length of the reference segment the cigar describes | |
| const ParsedCigar & | getParsedCigar () const |
| void | add (const CigarElement &e) |
| CigarElement & | operator[] (size_t i) |
| CigarElement & | back () |
| size_t | size () const |
| void | trancatePaddings () |
| Cigar | pack () const |
| Removes zero size section merges neighbor sections of the same type and returns a copy. | |
| bool | operator== (const Cigar &c) const |
Protected Member Functions | |
| void | push_back (const CigarElement &e) |
| void | add_back (const CigarElement &e) |
| merges the last and new elements if they have equal types | |
Protected Attributes | |
| bool | mergeNeighbours_ |
| bool | removeZeros_ |
| ParsedCigar | parsedCigar_ |
Friends | |
| std::ostream & | operator<< (std::ostream &out, const Cigar &cigar) |
Provides support for manipulations on SAM/BAM and CGI Evidence CIGAR.
1.6.2
