Commit 58ea2f53 authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.{h, cpp}: DEFAULT_MINIMIZE_WIDTH, DEFAULT_MINIMIZE_ONE_MARGIN

parent b4a5e5b5
......@@ -477,12 +477,11 @@ KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline, double threshold,
return ;
}
int pos = kaa.minimize(kmer, DEFAULT_MINIMIZE_ONE_MARGIN, DEFAULT_MINIMIZE_WIDTH);
segmented = true ;
because = reversed ? SEG_MINUS : SEG_PLUS ;
// 30 should be more than half of the window. Should we run this during getJunction(), once w is known ?
int pos = kaa.minimize(kmer, 30, 8);
info = "=" + string_of_int(c) + " @" + string_of_int(pos) ;
// getJunction() will be centered on pos
......
......@@ -46,6 +46,9 @@
be overriden by the command line by
providing a shorter -w*/
#define DEFAULT_MINIMIZE_WIDTH 12
#define DEFAULT_MINIMIZE_ONE_MARGIN 20
using namespace std;
using json = nlohmann::json;
......
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