Mercurial > repos > chrisd > testing
comparison gene_fraction/src/Sam.cpp @ 0:f95150c37d38 draft default tip
planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
| author | chrisd |
|---|---|
| date | Sun, 21 Feb 2016 23:31:55 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:f95150c37d38 |
|---|---|
| 1 #include "Sam.h" | |
| 2 #include "args.h" | |
| 3 #include "dir_util.h" | |
| 4 #include "alignment_util.h" | |
| 5 | |
| 6 #include <iostream> | |
| 7 #include <fstream> | |
| 8 | |
| 9 Sam::Sam(std::string sam_fp) : _sam_fp(sam_fp) {} | |
| 10 | |
| 11 void Sam::read_sam(cmd_args args) { | |
| 12 if(args.bam_stream) read_from_stdin(); | |
| 13 else read_from_file(args.sam_fp); | |
| 14 } | |
| 15 | |
| 16 void Sam::read_from_stdin() { | |
| 17 std::string line; | |
| 18 while(std::getline(std::cin, line)) { | |
| 19 if(line[0] == '@') continue; | |
| 20 alignment.push_back(line); | |
| 21 } | |
| 22 } | |
| 23 | |
| 24 void Sam::read_from_file(const std::string &sam_fp) { | |
| 25 std::ifstream in(sam_fp.c_str()); | |
| 26 if(!in) { | |
| 27 usage(); | |
| 28 exit(EXIT_FAILURE); | |
| 29 } | |
| 30 | |
| 31 std::string line; | |
| 32 while(getline(in, line)) { | |
| 33 if(line[0] == '@') continue; | |
| 34 if(is_good_alignment(line)) | |
| 35 alignment.push_back(line); | |
| 36 } | |
| 37 | |
| 38 in.close(); | |
| 39 } | |
| 40 | |
| 41 |