This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository nanopolish.
commit e3ac02838d4c1f135f9d052eb481ee61ab916b50 Author: Andreas Tille <[email protected]> Date: Fri Sep 1 08:37:38 2017 +0200 Refresh patches --- debian/patches/adjust-include-path.patch | 39 ++---------------- debian/patches/compiler-flags.patch | 20 ++------- debian/patches/external-libs.patch | 40 +++++++----------- debian/patches/fast5-0.5.6.patch | 33 --------------- debian/patches/fix-ftbfs-with-gcc6.patch | 14 ------- debian/patches/gcc-7.patch | 70 -------------------------------- debian/patches/reproducible.patch | 6 +-- debian/patches/series | 3 -- 8 files changed, 25 insertions(+), 200 deletions(-) diff --git a/debian/patches/adjust-include-path.patch b/debian/patches/adjust-include-path.patch index 44ce571..b54e934 100644 --- a/debian/patches/adjust-include-path.patch +++ b/debian/patches/adjust-include-path.patch @@ -4,46 +4,13 @@ Description: Adjust #include statements Author: Afif Elghraoui <[email protected]> Forwarded: https://github.com/jts/nanopolish/pull/33 Last-Update: 2016-08-11 ---- nanopolish.orig/src/nanopolish_poremodel.cpp -+++ nanopolish/src/nanopolish_poremodel.cpp -@@ -11,7 +11,7 @@ - #include <sstream> - #include <cstring> - #include <bits/stl_algo.h> --#include "../fast5/src/fast5.hpp" -+#include <fast5.hpp> - - void PoreModel::bake_gaussian_parameters() - { ---- nanopolish.orig/src/nanopolish_poremodel.h -+++ nanopolish/src/nanopolish_poremodel.h -@@ -15,7 +15,7 @@ - #include <string> - #include <map> - #include "nanopolish_model_names.h" --#include "../fast5/src/fast5.hpp" -+#include <fast5.hpp> - - // - struct PoreModelStateParams ---- nanopolish.orig/src/nanopolish_squiggle_read.cpp -+++ nanopolish/src/nanopolish_squiggle_read.cpp -@@ -11,7 +11,7 @@ - #include "nanopolish_squiggle_read.h" - #include "nanopolish_pore_model_set.h" - #include "nanopolish_methyltrain.h" --#include "src/fast5.hpp" -+#include <fast5.hpp> - - // - SquiggleRead::SquiggleRead(const std::string& name, const std::string& path, const uint32_t flags) : ---- nanopolish.orig/src/nanopolish_methyltrain.cpp -+++ nanopolish/src/nanopolish_methyltrain.cpp +--- a/src/nanopolish_methyltrain.cpp ++++ b/src/nanopolish_methyltrain.cpp @@ -42,7 +42,7 @@ #include "logger.hpp" #include "nanopolish_scorereads.h" --#include "../eigen/Eigen/Dense" +-#include "Eigen/Dense" +#include <eigen3/Eigen/Dense> extern float g_p_skip, g_p_skip_self, g_p_bad, g_p_bad_self; diff --git a/debian/patches/compiler-flags.patch b/debian/patches/compiler-flags.patch index 6e32878..cf29691 100644 --- a/debian/patches/compiler-flags.patch +++ b/debian/patches/compiler-flags.patch @@ -4,24 +4,12 @@ Description: Allow adding settings to standard compiler flags Author: Afif Elghraoui <[email protected]> Forwarded: no Last-Update: 2016-08-11 ---- nanopolish.orig/Makefile -+++ nanopolish/Makefile -@@ -9,9 +9,9 @@ - - #Basic flags every build needs - LIBS=-lz --CXXFLAGS = -g -O3 -+CXXFLAGS += -g -O3 - CXXFLAGS += -std=c++11 -fopenmp --CFLAGS=-O3 -+CFLAGS += -O3 - CXX=g++ - CC=gcc - HDF5=install -@@ -108,11 +108,11 @@ +--- a/Makefile ++++ b/Makefile +@@ -120,11 +120,11 @@ include .depend # Link main executable - $(PROGRAM): src/main/nanopolish.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(EIGEN) + $(PROGRAM): src/main/nanopolish.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(EIGEN_CHECK) - $(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS) + $(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS) $(LDFLAGS) diff --git a/debian/patches/external-libs.patch b/debian/patches/external-libs.patch index 3f11455..0c3f382 100644 --- a/debian/patches/external-libs.patch +++ b/debian/patches/external-libs.patch @@ -4,40 +4,30 @@ Description: Set up build system to use externally installed libraries Author: Afif Elghraoui <[email protected]> Forwarded: not-needed Last-Update: 2016-01-18 ---- nanopolish.orig/Makefile -+++ nanopolish/Makefile -@@ -14,7 +14,6 @@ - CFLAGS += -O3 - CXX=g++ - CC=gcc +--- a/Makefile ++++ b/Makefile +@@ -16,7 +16,6 @@ CXX ?= g++ + CC ?= gcc + + # Change the value of HDF5 or EIGEN below to any value to disable compilation of bundled HDF5 code -HDF5=install + EIGEN=install # Check operating system, OSX doesn't have -lrt - UNAME_S := $(shell uname -s) -@@ -34,9 +33,7 @@ - LIBS += -lhdf5 +@@ -46,14 +45,13 @@ else endif --# Bulild and link the libhts submodule + # Build and link the libhts submodule -HTS_LIB=./htslib/libhts.a -HTS_INCLUDE=-I./htslib +LIBS += -lhts # Include the header-only fast5 library - FAST5_INCLUDE=-I./fast5 -@@ -68,13 +65,10 @@ - cd hdf5-1.8.14; ./configure --enable-threadsafe --prefix=`pwd`/..; make; make install - - --# Download and install eigen if not already downloaded --EIGEN=eigen/INSTALL -+# Don't use external EIGEN -+EIGEN= + FAST5_INCLUDE=-I./fast5/src - $(EIGEN): -- wget http://bitbucket.org/eigen/eigen/get/3.2.5.tar.bz2 -- tar -xjvf 3.2.5.tar.bz2 -- mv eigen-eigen-bdd17ee3b1b3 eigen + # Include the header-only eigen library +-EIGEN_INCLUDE=-I./eigen/ ++EIGEN_INCLUDE=-I/usr/include/eigen3/ - # - # Source files + # Include the src subdirectories + NP_INCLUDE=$(addprefix -I./, $(SUBDIRS)) diff --git a/debian/patches/fast5-0.5.6.patch b/debian/patches/fast5-0.5.6.patch deleted file mode 100644 index 4bffb27..0000000 --- a/debian/patches/fast5-0.5.6.patch +++ /dev/null @@ -1,33 +0,0 @@ -Description: Fix compatibility with fast5 0.5.6 -Author: Afif Elghraoui <[email protected]> -Forwarded: https://github.com/jts/nanopolish/pull/61 -Last-Update: 2016-08-11 ---- nanopolish.orig/src/nanopolish_squiggle_read.cpp -+++ nanopolish/src/nanopolish_squiggle_read.cpp -@@ -119,7 +119,7 @@ - } - } - -- read_sequence = f_p->get_basecall_seq(basecall_group, read_type); -+ read_sequence = f_p->get_basecall_seq(read_type, basecall_group); - - // Load PoreModel for both strands - std::vector<EventRangeForBase> event_maps_1d[NUM_STRANDS]; -@@ -139,7 +139,7 @@ - } - - // Load the events for this strand -- std::vector<fast5::Event_Entry> f5_events = f_p->get_basecall_events(event_group, si); -+ std::vector<fast5::Event_Entry> f5_events = f_p->get_basecall_events(si, event_group); - - // copy events - events[si].resize(f5_events.size()); -@@ -161,7 +161,7 @@ - // or discarded if this is a 2D read - - // NB we use event_group in this call rather than basecall_group as we want the 1D basecalls that match the events -- read_sequences_1d[si] = f_p->get_basecall_seq(event_group, si == 0 ? SRT_TEMPLATE : SRT_COMPLEMENT); -+ read_sequences_1d[si] = f_p->get_basecall_seq(si == 0 ? SRT_TEMPLATE : SRT_COMPLEMENT, event_group); - event_maps_1d[si] = build_event_map_1d(f_p, read_sequences_1d[si], si, f5_events); - std::vector<EventAlignment> alignment = - get_eventalignment_for_1d_basecalls(read_sequences_1d[si], event_maps_1d[si], 5, si); diff --git a/debian/patches/fix-ftbfs-with-gcc6.patch b/debian/patches/fix-ftbfs-with-gcc6.patch deleted file mode 100644 index 534261f..0000000 --- a/debian/patches/fix-ftbfs-with-gcc6.patch +++ /dev/null @@ -1,14 +0,0 @@ -Description: fix build with GCC6 -Author: Sascha Steinbiss <[email protected]> ---- nanopolish.orig/src/common/nanopolish_variant.cpp -+++ nanopolish/src/common/nanopolish_variant.cpp -@@ -29,7 +29,8 @@ - const std::string& haplotype) - { - AlnParam par = aln_param_nt2nt; -- par.band_width = std::max(20, abs(reference.size() - haplotype.size()) * 2); -+ size_t difference = std::abs(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); - - // Make aligned strings where gaps are padded with '-' diff --git a/debian/patches/gcc-7.patch b/debian/patches/gcc-7.patch deleted file mode 100644 index a8bda2b..0000000 --- a/debian/patches/gcc-7.patch +++ /dev/null @@ -1,70 +0,0 @@ -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 - ---- a/src/alignment/nanopolish_eventalign.cpp -+++ b/src/alignment/nanopolish_eventalign.cpp -@@ -679,7 +679,7 @@ std::vector<EventAlignment> align_read_t - // over very large deletions wrt to the reference. The effect of this - // 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(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) { diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch index a96a7f3..2191158 100644 --- a/debian/patches/reproducible.patch +++ b/debian/patches/reproducible.patch @@ -2,9 +2,9 @@ Description: make build reproducible This patch enforces stable input file ordering w.r.t. source file gathering via Make's 'wildcard' directive. Author: Sascha Steinbiss <[email protected]> ---- nanopolish.orig/Makefile -+++ nanopolish/Makefile -@@ -75,8 +75,8 @@ +--- a/Makefile ++++ b/Makefile +@@ -91,8 +91,8 @@ eigen/INSTALL: # # Find the source files by searching subdirectories diff --git a/debian/patches/series b/debian/patches/series index b30a50b..dacdb9f 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -2,7 +2,4 @@ adjust-include-path.patch compiler-flags.patch external-libs.patch add-shebang-to-script.patch -fix-ftbfs-with-gcc6.patch reproducible.patch -fast5-0.5.6.patch -gcc-7.patch -- 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
