Mercurial > repos > chrisd > testshed
annotate 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 |
parents | |
children |
rev | line source |
---|---|
0
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
1 #include <iostream> |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
2 #include <string> |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
3 #include <vector> |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
4 |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
5 #include "args.h" |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
6 #include "Fasta.h" |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
7 #include "FastaRecord.h" |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
8 #include "Sam.h" |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
9 #include "SnipDriver.h" |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
10 |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
11 using namespace std; |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
12 |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
13 void print_fasta(const Fasta &f) { |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
14 for(const auto &record: f.records) { |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
15 cout << record.gene_id() << endl; |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
16 cout << record.gene() << endl; |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
17 } |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
18 } |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
19 |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
20 void print_sam(const Sam &s) { |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
21 for(const auto &alignment: s.alignments) { |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
22 cout << alignment.alignment() << endl; |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
23 } |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
24 } |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
25 |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
26 int main(int argc, const char *argv[]) { |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
27 cmd_args arg; |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
28 arg = parse_command_line(argc, argv); |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
29 |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
30 Fasta f(arg.amr_fp); |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
31 f.read_fasta(arg.amr_fp); |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
32 |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
33 Sam s(arg.sam_fp); |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
34 if(arg.samse) { |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
35 s.read_se_sam(arg.sam_fp, arg.best); |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
36 } |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
37 else { |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
38 s.read_pe_sam(arg.sam_fp, arg.best); |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
39 } |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
40 |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
41 run(f.records, s.alignments, arg); |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
42 write_snips(f.records, arg.out_fp); |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
43 |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
44 |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
45 return 0; |
0fd352f62446
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
parents:
diff
changeset
|
46 } |