This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository nanopolish.
commit 1d012e170f5984b6de87499d8f704cdfd9489095 Author: Andreas Tille <[email protected]> Date: Fri Sep 1 07:25:55 2017 +0200 More abs() replacements --- debian/patches/gcc-7.patch | 58 ++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 56 insertions(+), 2 deletions(-) diff --git a/debian/patches/gcc-7.patch b/debian/patches/gcc-7.patch index b7fa956..a8bda2b 100644 --- a/debian/patches/gcc-7.patch +++ b/debian/patches/gcc-7.patch @@ -1,4 +1,5 @@ -Autor: Andreas Tille <[email protected]> +Autor: Andreas Tille <[email protected]>, + Walter Landry <[email protected]> last-Update: Thu, 31 Aug 2017 23:33:00 +0200 Bug-Debian: https://bugs.debian.org/853568 Description: Make sure abs() gets int arguments @@ -10,7 +11,60 @@ Description: Make sure abs() gets int arguments // is that we can get segments that have very few alignable events. We // just stop processing them for now - if(abs(input.event_start_idx - input.event_stop_idx) < 2) -+ if(abs(int(input.event_start_idx) - int(input.event_stop_idx)) < 2) ++ if(abs(static_cast<int>((input.event_start_idx - input.event_stop_idx)) < 2) break; input.strand = params.strand_idx; +--- a/src/common/nanopolish_variant.cpp ++++ b/src/common/nanopolish_variant.cpp +@@ -29,7 +29,7 @@ std::vector<Variant> extract_variants(co + const std::string& haplotype) + { + AlnParam par = aln_param_nt2nt; +- size_t difference = std::abs(reference.size() - haplotype.size()); ++ size_t difference = std::abs(static_cast<ptrdiff_t>(reference.size() - haplotype.size())); + par.band_width = std::max((size_t) 20, difference * 2); + AlnAln* aln = aln_stdaln(reference.c_str(), haplotype.c_str(), &par, 1, 1); + +--- a/src/hmm/nanopolish_profile_hmm.cpp ++++ b/src/hmm/nanopolish_profile_hmm.cpp +@@ -290,7 +290,7 @@ void print_alignment(const std::string& + double time_start = data.read->events[data.strand][data.event_start_idx].start_time; + double time_end = data.read->events[data.strand][data.event_stop_idx].start_time; + double total_duration = fabs(time_start - time_end); +- double num_events = abs(data.event_start_idx - data.event_stop_idx) + 1; ++ double num_events = abs(static_cast<int>(data.event_start_idx - data.event_stop_idx)) + 1; + double final_lp = alignment[alignment.size() - 1].l_fm; + double mean_lp = final_lp / num_events; + +--- a/src/nanopolish_call_variants.cpp ++++ b/src/nanopolish_call_variants.cpp +@@ -392,7 +392,7 @@ void print_debug_stats(const std::string + const HMMInputData& data = event_sequences[i]; + + // summarize score +- double num_events = abs(data.event_start_idx - data.event_stop_idx) + 1; ++ double num_events = abs(static_cast<int>(data.event_start_idx - data.event_stop_idx)) + 1; + double base_score = profile_hmm_score(base_haplotype.get_sequence(), data, alignment_flags); + double called_score = profile_hmm_score(called_haplotype.get_sequence(), data, alignment_flags); + double base_avg = base_score / num_events; +@@ -548,7 +548,7 @@ Haplotype fix_homopolymers(const Haploty + assert(kmer_size == 6); + + // skip small event regions +- if( abs(event_sequences[j].event_start_idx - event_sequences[j].event_stop_idx) < 10) { ++ if( abs(static_cast<int>(event_sequences[j].event_start_idx - event_sequences[j].event_stop_idx)) < 10) { + continue; + } + +--- a/src/nanopolish_consensus.cpp ++++ b/src/nanopolish_consensus.cpp +@@ -531,7 +531,7 @@ void filter_outlier_data(std::vector<HMM + const HMMInputData& rs = input[ri]; + + double curr = score_sequence(sequence, rs); +- double n_events = abs(rs.event_start_idx - rs.event_stop_idx) + 1.0f; ++ double n_events = abs(static_cast<int>(rs.event_start_idx - rs.event_stop_idx)) + 1.0f; + double lp_per_event = curr / n_events; + + if(opt::verbose >= 1) { -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/nanopolish.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
