Commit c23b5d20 authored by Mathieu Giraud's avatar Mathieu Giraud

core/germline.cpp: insert D k-mers in the index

There are sometimes common k-mers between D and V/J genes (this was at least
the case for IGH with -t 0), and this may give badly positioned windows.
Now all D k-mers are stored in the index, marking these k-mers as AMBIGUOUS.
Note that it is the first time that the D germline is actually used in the KmerSegmenter.
parent 493870ca
......@@ -16,7 +16,7 @@ void Germline::init(string _code, char _shortcut,
affect_3 = "J" ;
affect_5 = string(1, toupper(shortcut)) + "-" + code + "V";
affect_4 = ""; // string(1, 14 + shortcut) + "-" + code + "D";
affect_4 = string(1, 14 + shortcut) + "-" + code + "D";
affect_3 = string(1, tolower(shortcut)) + "-" + code + "J";
delta_min = _delta_min ;
......@@ -103,11 +103,9 @@ void Germline::set_index(IKmerStore<KmerAffect> *_index)
void Germline::update_index(IKmerStore<KmerAffect> *_index)
{
if (!_index) _index = index ;
_index->insert(rep_5, affect_5, max_indexing);
if (affect_4.size())
_index->insert(rep_4, affect_4);
_index->insert(rep_5, affect_5, max_indexing);
_index->insert(rep_4, affect_4);
_index->insert(rep_3, affect_3, -max_indexing);
}
......
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