Mercurial > repos > chrisd > testshed
comparison gene_fraction/src/main.cpp @ 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 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:0fd352f62446 |
---|---|
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 } |