/** Record the trimmed contigs. */
static void recordTrimmedContigs(
ContigPath::const_iterator first,
ContigPath::const_iterator last)
{
for (ContigPath::const_iterator it = first; it != last; ++it)
if (!it->ambiguous())
s_trimmedContigs.push_back(it->contigIndex());
}
/** Return the set of contigs that appear more than once in a single
* solution.
*/
static set<ContigID> findRepeats(ContigID seed,
const ContigPaths& solutions)
{
set<ContigID> repeats;
for (ContigPaths::const_iterator solIt = solutions.begin();
solIt != solutions.end(); ++solIt) {
map<ContigID, unsigned> count;
count[seed]++;
for (ContigPath::const_iterator it = solIt->begin();
it != solIt->end(); ++it)
count[it->contigIndex()]++;
for (map<ContigID, unsigned>::const_iterator
it = count.begin(); it != count.end(); ++it)
if (it->second > 1)
repeats.insert(it->first);
}
return repeats;
}
/** Return all contigs that are tandem repeats, identified as those
* contigs that appear more than once in a single path.
*/
static set<ContigID> findRepeats(const ContigPathMap& paths)
{
set<ContigID> repeats;
for (ContigPathMap::const_iterator pathIt = paths.begin();
pathIt != paths.end(); ++pathIt) {
const ContigPath& path = pathIt->second;
map<ContigID, unsigned> count;
for (ContigPath::const_iterator it = path.begin();
it != path.end(); ++it)
if (!it->ambiguous())
count[it->contigIndex()]++;
for (map<ContigID, unsigned>::const_iterator
it = count.begin(); it != count.end(); ++it)
if (it->second > 1)
repeats.insert(it->first);
}
return repeats;
}