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annotate gene_fraction/src/Alignments.cpp @ 0:0fd352f62446 draft default tip

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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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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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1 #include "Alignments.h"
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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2 #include "int_util.h"
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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4 #include <boost/algorithm/string.hpp>
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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6 #include <iostream>
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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7 #include <sstream>
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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9 Alignments::Alignments(std::string alignment) : _alignment(alignment) {
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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10 fill_alignment_fields(alignment);
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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11 }
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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13 void Alignments::fill_alignment_fields(const std::string &alignment) {
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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14 std::istringstream ss(alignment);
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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15 ss >> field.QNAME >> field.FLAG >> field.RNAME >> field.POS >>
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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16 field.MAPQ >> field.CIGAR >> field.RNEXT >> field.PNEXT >>
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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17 field.TLEN >> field.SEQ >> field.QUAL;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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18 }
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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20 std::vector<std::pair<int,char>> Alignments::cigar() {
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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21 return get_cigar_operations(field.CIGAR);
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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22 }
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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24 std::vector<std::pair<int,char>> Alignments::get_cigar_operations(const std::string &cigar) {
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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25 std::vector<std::pair<int,char>> p;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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26 int count;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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27 char operation;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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29 std::istringstream ss(cigar);
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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30 while(ss >> count >> operation) {
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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31 p.push_back(std::make_pair(count, operation));
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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32 }
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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34 return p;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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35 }