Mercurial > repos > chrisd > testing

comparison gene_fraction/src/main.cpp @ 0:f95150c37d38 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 <string>
2 #include <iostream>
3 #include <vector>
4
5 #include "int_util.h"
6 #include "dir_util.h"
7 #include "args.h"
8 #include "Fasta.h"
9 #include "Sam.h"
10 #include "SamRatio.h"
11
12 using namespace std;
13
14 int main(int argc, char *argv[]) {
15 cmd_args args;
16 args = parse_command_line(argc, argv);
17
18 Fasta f(args.amr_fp);
19 f.read_fasta(args.amr_fp);
20
21 if(args.sam_dir) {
22 list<string> sam_files = parse_sam_dir(args.sam_fp);
23 for(auto &fn : sam_files) {
24 args.sam_fp = fn;
25 Sam s(args.sam_fp);
26 s.read_sam(args);
27 generate_samples(f.records, s.alignment, args);
28 }
29 }
30 else {
31 Sam s(args.sam_fp);
32 s.read_sam(args);
33 generate_samples(f.records, s.alignment, args);
34 }
35
36 return 0;
37 }