Mercurial > repos > chrisd > testshed
diff snp_caller/src/Sam.h @ 0:0fd352f62446 draft default tip
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
| author | chrisd |
|---|---|
| date | Sun, 21 Feb 2016 06:05:24 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snp_caller/src/Sam.h Sun Feb 21 06:05:24 2016 -0500 @@ -0,0 +1,23 @@ +#ifndef SAM_H +#define SAM_H + +#include "Alignment.h" + +class Sam { +public: + Sam(std::string sam_fp); + void read_se_sam(const std::string &sam_fp, bool best); + void read_pe_sam(const std::string &sam_fp, bool best); + static void sort_by_qname(std::vector<Alignment> &v); + + std::vector<Alignment> alignments; +private: + std::string _sam_fp; + +}; + + + +#endif //SAM_H + +