From c1ac9fac86716100d31dc82f6661ef798731e107 Mon Sep 17 00:00:00 2001 From: Mathieu Giraud Date: Thu, 11 Jun 2015 21:44:33 +0200 Subject: [PATCH] core/segment.cpp, core/kmerstore.h: MAX1U, report information through FineSegmenter --- algo/core/kmerstore.h | 2 +- algo/core/segment.cpp | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/algo/core/kmerstore.h b/algo/core/kmerstore.h index e6d386ad8..514f4ae13 100644 --- a/algo/core/kmerstore.h +++ b/algo/core/kmerstore.h @@ -333,7 +333,7 @@ string IKmerStore::getLabel(T kmer) const { for (typename list< pair >::const_iterator it = labels.begin(); it != labels.end(); ++it) if (it->first == kmer) return it->second ; - return "" ; + return "?" ; } // .getResults() diff --git a/algo/core/segment.cpp b/algo/core/segment.cpp index 69cc66ac3..7e6899fa4 100644 --- a/algo/core/segment.cpp +++ b/algo/core/segment.cpp @@ -642,9 +642,10 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c) if (!germline->rep_5.size() || !germline->rep_3.size()) { - // We check whether this sequence is segmented with MAX12 (with default e-value parameters) + // We check whether this sequence is segmented with MAX12 or MAX1U (with default e-value parameters) KmerSegmenter *kseg = new KmerSegmenter(seq, germline, THRESHOLD_NB_EXPECTED, 1); - if (kseg->isSegmented() && (!strcmp(germline->code.c_str(), PSEUDO_GERMLINE_MAX12))) + if (kseg->isSegmented() && ((!strcmp(germline->code.c_str(), PSEUDO_GERMLINE_MAX12)) + || !strcmp(germline->code.c_str(), PSEUDO_GERMLINE_MAX1U))) { reversed = kseg->isReverse(); -- GitLab