Commit 2cac4cd1 authored by Mathieu Giraud's avatar Mathieu Giraud

germline.cpp: mark_cross_germlines_as_ambiguous(), skip VdJa

parent e90c48b8
......@@ -267,10 +267,16 @@ void MultiGermline::out_stats(ostream &out)
/* Mark k-mers common to several germlines as ambiguous */
void MultiGermline::mark_cross_germlines_as_ambiguous()
{
string VdJa = "VdJa";
for (list<Germline*>::const_iterator it = germlines.begin(); it != germlines.end(); ++it)
{
Germline *germline = *it ;
cout << *germline << ":" ;
// Skip VdJa
if (!(germline->code.compare(VdJa)))
continue;
for (list<Germline*>::const_iterator it2 = germlines.begin(); it2 != germlines.end(); ++it2)
{
......@@ -281,6 +287,10 @@ void MultiGermline::mark_cross_germlines_as_ambiguous()
// Skip germlines on a same system, such as 'D' (TRD) and 'd' (TRD+)
if (toupper(germline2->shortcut) == toupper(germline->shortcut))
continue;
// Skip VdJa
if (!(germline2->code.compare(VdJa)))
continue;
germline->mark_as_ambiguous(germline2);
}
......
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