diff --git a/src/nam.cpp b/src/nam.cpp index b0f84886..7ecf43bd 100644 --- a/src/nam.cpp +++ b/src/nam.cpp @@ -16,9 +16,9 @@ void add_to_hits_per_ref( int query_end, bool is_rc, const StrobemerIndex& index, - size_t position, - int min_diff + size_t position ) { + int min_diff = std::numeric_limits::max(); for (const auto hash = index.get_hash(position); index.get_hash(position) == hash; ++position) { int ref_start = index.get_strobe1_position(position); int ref_end = ref_start + index.strobe2_offset(position) + index.k(); @@ -160,7 +160,7 @@ std::pair> find_nams( continue; } nr_good_hits++; - add_to_hits_per_ref(hits_per_ref, q.start, q.end, q.is_reverse, index, position, 100'000); + add_to_hits_per_ref(hits_per_ref, q.start, q.end, q.is_reverse, index, position); } } float nonrepetitive_fraction = total_hits > 0 ? ((float) nr_good_hits) / ((float) total_hits) : 1.0; @@ -171,6 +171,7 @@ std::pair> find_nams( /* * Find a query’s NAMs, using also some of the randstrobes that occur more often * than filter_cutoff. + * */ std::vector find_nams_rescue( const QueryRandstrobeVector &query_randstrobes, @@ -218,7 +219,7 @@ std::vector find_nams_rescue( if ((rh.count > filter_cutoff && cnt >= 5) || rh.count > 1000) { break; } - add_to_hits_per_ref(hits_per_ref, rh.query_start, rh.query_end, rh.is_rc, index, rh.position, 1000); + add_to_hits_per_ref(hits_per_ref, rh.query_start, rh.query_end, rh.is_rc, index, rh.position); cnt++; } }