Commit 6deddb42 authored by Mathieu Giraud's avatar Mathieu Giraud

core/windowExtractor.cpp: display tested germline together with the case of unsegmentation

Now KmerSegmenter.segmented_germline always contains the last tested germline, even
when it is not actually segmented.
parent a8df78ec
......@@ -176,6 +176,7 @@ KmerSegmenter::KmerSegmenter(Sequence seq, MultiGermline *multigermline)
for (list<Germline*>::const_iterator it = multigermline->germlines.begin(); it != multigermline->germlines.end(); ++it)
{
Germline *germline = *it ;
segmented_germline = germline;
int s = (size_t)germline->index->getS() ;
int length = sequence.length() ;
......@@ -221,7 +222,6 @@ KmerSegmenter::KmerSegmenter(Sequence seq, MultiGermline *multigermline)
if (segmented)
{
// Yes, it is segmented
segmented_germline = germline;
germline->stats.insert(length);
reversed = (strand == -1);
......
......@@ -46,7 +46,7 @@ WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *mult
} else if (out_unsegmented) {
*out_unsegmented << reads->getSequence();
*out_unsegmented << "#" << segmented_mesg[seg.getSegmentationStatus()] << endl;
*out_unsegmented << "#" << segmented_mesg[seg.getSegmentationStatus()] << " " << seg.segmented_germline->code << endl;
if (seg.getSegmentationStatus() != UNSEG_TOO_SHORT) {
*out_unsegmented << seg.getKmerAffectAnalyser()->toString() << endl;
}
......
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