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

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planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
author chrisd
date Sun, 21 Feb 2016 23:31:55 -0500
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-1:000000000000 0:f95150c37d38
1 #include "Alignments.h"
2 #include "int_util.h"
3
4 #include <boost/algorithm/string.hpp>
5
6 #include <iostream>
7 #include <sstream>
8
9 Alignments::Alignments(std::string alignment) : _alignment(alignment) {
10 fill_alignment_fields(alignment);
11 }
12
13 void Alignments::fill_alignment_fields(const std::string &alignment) {
14 std::istringstream ss(alignment);
15 ss >> field.QNAME >> field.FLAG >> field.RNAME >> field.POS >>
16 field.MAPQ >> field.CIGAR >> field.RNEXT >> field.PNEXT >>
17 field.TLEN >> field.SEQ >> field.QUAL;
18 }
19
20 std::vector<std::pair<int,char>> Alignments::cigar() {
21 return get_cigar_operations(field.CIGAR);
22 }
23
24 std::vector<std::pair<int,char>> Alignments::get_cigar_operations(const std::string &cigar) {
25 std::vector<std::pair<int,char>> p;
26 int count;
27 char operation;
28
29 std::istringstream ss(cigar);
30 while(ss >> count >> operation) {
31 p.push_back(std::make_pair(count, operation));
32 }
33
34 return p;
35 }