Commit a8df78ec authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

core/segment.{h,cpp}: both V and J kmers must be above DETECT_THRESHOLD to...

core/segment.{h,cpp}: both V and J kmers must be above DETECT_THRESHOLD to flag the germline as 'detected'

This reverts the idea of 41b4f071, but still uses a 'detected' flag.
This flag tells us whether we should continue to the remaining germlines.
In the case of incomplete rearrangements, we certainly want to continue even if we have
many V or many J (but now both of them).
Tests d2a0dbd5 are now passing.

Note that we don't run this test when strand == 2, this should be changed.
parent 3b37a335
......@@ -215,9 +215,7 @@ KmerSegmenter::KmerSegmenter(Sequence seq, MultiGermline *multigermline)
strand = 2;
// Are there enoguh V/J to assert that this was the correct germline (and thus that we won't test other ones) ?
detected = (nb_strand[0] + nb_strand[1] >= DETECT_THRESHOLD);
detected = false ;
computeSegmentation(strand, germline);
if (segmented)
......@@ -275,6 +273,11 @@ void KmerSegmenter::computeSegmentation(int strand, Germline* germline) {
max = kaa->getMaximum(KmerAffect(germline->affect_3, -1),
KmerAffect(germline->affect_5, -1));
// We labeled it detected if there were both enough affect_5 and enough affect_3
detected = (max.nb_before_left + max.nb_before_right >= DETECT_THRESHOLD)
&& (max.nb_after_left + max.nb_after_right >= DETECT_THRESHOLD);
if (! max.max_found) {
if ((strand == 1 && max.nb_before_left == 0)
|| (strand == -1 && max.nb_after_right == 0))
......@@ -17,7 +17,7 @@
strand and the other, to safely attribute a
segment to a given strand */
#define DETECT_THRESHOLD 10 /* If the number of total V/J affectations
#define DETECT_THRESHOLD 5 /* If the number of both V and J affectations
is above this threshold, then the sequence
will be labeled as 'detected', and, if it
not segmented, the remaining germlines will
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