Commit e59972d4 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

windowExtractor.cpp: display kmer affect for segmented sequences with '-u' option is set

fixes 699675262f
parent 15e0f4e1
......@@ -31,9 +31,13 @@ WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, IKmerStore<KmerAffe
stats_length[TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW] += seg.getSequence().sequence.length() ;
}
if (out_segmented)
if (out_segmented) {
*out_segmented << seg ; // KmerSegmenter output (V/N/J)
*out_segmented << seg.getKmerAffectAnalyser()->toString() << endl;
if (out_unsegmented)
*out_segmented << seg.getKmerAffectAnalyser()->toString() << endl;
}
} else if (out_unsegmented) {
*out_unsegmented << reads->getSequence();
*out_unsegmented << "#" << segmented_mesg[seg.getSegmentationStatus()] << endl;
......
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