Commit 7c07b74e authored by Mathieu Giraud's avatar Mathieu Giraud

core/germline.{h,cpp}: MultiGermline.mark_cross_germlines_as_ambiguous()

In each of the germline, mark as ambiguous the k-mers appearing in another germline.
parent 37fc6576
......@@ -263,6 +263,27 @@ void MultiGermline::out_stats(ostream &out)
}
}
/* Mark k-mers common to several germlines as ambiguous */
void MultiGermline::mark_cross_germlines_as_ambiguous()
{
for (list<Germline*>::const_iterator it = germlines.begin(); it != germlines.end(); ++it)
{
Germline *germline = *it ;
cout << *germline << ":" ;
for (list<Germline*>::const_iterator it2 = germlines.begin(); it2 != germlines.end(); ++it2)
{
Germline *germline2 = *it2 ;
if (germline2 == germline)
continue ;
germline->mark_as_ambiguous(germline2);
}
cout << endl;
}
}
ostream &operator<<(ostream &out, const MultiGermline &multigermline)
{
......
......@@ -94,6 +94,8 @@ class MultiGermline {
void insert_in_one_index(IKmerStore<KmerAffect> *_index);
void build_with_one_index(string seed);
void mark_cross_germlines_as_ambiguous();
void out_stats(ostream &out);
};
......
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