← Back to branch summary

~ubuntu-branches/ubuntu/saucy/abyss/saucy

« back to all changes in this revision

Viewing changes to ParseAligns/abyss-fixmate.cc

  • Committer: Package Import Robot
  • Author(s): Shaun Jackman
  • Date: 2011-09-11 10:00:13 UTC
  • mfrom: (1.1.1 upstream)
  • Revision ID: package-import@ubuntu.com-20110911100013-oa4m5fi036mjuwc8
Tags: 1.3.0-1
* New upstream release.
* Add libboost-graph-dev to Build-Depends.

Show diffs side-by-side

added added

removed removed

Lines of Context:
ParseAligns/abyss-fixmate.cc
23
23
PROGRAM " (" PACKAGE_NAME ") " VERSION "\n"
24
24
"Written by Shaun Jackman.\n"
25
25
"\n"
26
 
"Copyright 2010 Canada's Michael Smith Genome Science Centre\n";
 
26
"Copyright 2011 Canada's Michael Smith Genome Science Centre\n";
27
27
 
28
28
static const char USAGE_MESSAGE[] =
29
29
"Usage: " PROGRAM " [OPTION]... [FILE]...\n"
95
95
                // Different targets.
96
96
                stats.numDifferent++;
97
97
                fixMate(a0, a1);
 
98
                // Set the mapping quality of both reads to their minimum.
 
99
                a0.mapq = a1.mapq = min(a0.mapq, a1.mapq);
98
100
                cout << a0 << '\n' << a1 << '\n';
99
101
        } else if (a0.isReverse() == a1.isReverse()) {
100
102
                // Same target, FF orientation.
148
150
        pair<Alignments::iterator, bool> it = map.insert(
149
151
                        make_pair(sam.qname, sam));
150
152
        if (!it.second) {
 
153
#if SAM_SEQ_QUAL
 
154
                SAMRecord& a0 = it.first->second;
 
155
#else
151
156
                SAMRecord a0(it.first->second, it.first->first);
 
157
#endif
152
158
                handlePair(a0, sam);
153
159
                map.erase(it.first);
154
160
        }