comparison snp_caller/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
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-1:000000000000 0:0fd352f62446
1 #include <iostream>
2 #include <string>
3 #include <vector>
4
5 #include "args.h"
6 #include "Fasta.h"
7 #include "FastaRecord.h"
8 #include "Sam.h"
9 #include "SnipDriver.h"
10
11 using namespace std;
12
13 void print_fasta(const Fasta &f) {
14 for(const auto &record: f.records) {
15 cout << record.gene_id() << endl;
16 cout << record.gene() << endl;
17 }
18 }
19
20 void print_sam(const Sam &s) {
21 for(const auto &alignment: s.alignments) {
22 cout << alignment.alignment() << endl;
23 }
24 }
25
26 int main(int argc, const char *argv[]) {
27 cmd_args arg;
28 arg = parse_command_line(argc, argv);
29
30 Fasta f(arg.amr_fp);
31 f.read_fasta(arg.amr_fp);
32
33 Sam s(arg.sam_fp);
34 if(arg.samse) {
35 s.read_se_sam(arg.sam_fp, arg.best);
36 }
37 else {
38 s.read_pe_sam(arg.sam_fp, arg.best);
39 }
40
41 run(f.records, s.alignments, arg);
42 write_snips(f.records, arg.out_fp);
43
44
45 return 0;
46 }