[med-svn] [spades] 03/04: new upstream version
Sascha Steinbiss
satta at debian.org
Sun Sep 10 04:33:46 UTC 2017
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch next311
in repository spades.
commit 8e159d8faa39763c84a4731c0d3a0b5712b83173
Author: Sascha Steinbiss <satta at debian.org>
Date: Sat Sep 9 16:00:42 2017 +0200
new upstream version
---
debian/changelog | 6 +
debian/patches/0003_accept-system-bwa.patch | 16 +--
debian/patches/0111_use_full_config_dirs.patch | 8 +-
debian/patches/0114_use_debian_provided_libs.patch | 134 ++++-----------------
debian/patches/gcc7.patch | 8 +-
debian/patches/spelling | 32 ++---
6 files changed, 59 insertions(+), 145 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 8509830..818e7b7 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+spades (3.11.0+dfsg-1) unstable; urgency=medium
+
+ * New upstream release.
+
+ -- Sascha Steinbiss <satta at debian.org> Sun, 03 Sep 2017 22:56:54 +0200
+
spades (3.10.1+dfsg-3) unstable; urgency=medium
* Fix FTBFS with GCC 7.
diff --git a/debian/patches/0003_accept-system-bwa.patch b/debian/patches/0003_accept-system-bwa.patch
index fa2e718..0fb3707 100644
--- a/debian/patches/0003_accept-system-bwa.patch
+++ b/debian/patches/0003_accept-system-bwa.patch
@@ -13,9 +13,9 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
In case you consider taking over the patch I'd suggest to take it over into
some common import file.
---- spades.orig/src/spades_pipeline/support.py
-+++ spades/src/spades_pipeline/support.py
-@@ -58,6 +58,22 @@
+--- a/src/spades_pipeline/support.py
++++ b/src/spades_pipeline/support.py
+@@ -63,6 +63,22 @@
sys.stdout.write("\n\n" + prefix + " " + warn_str + "\n\n\n")
sys.stdout.flush()
@@ -37,8 +37,8 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
+ return None
def check_python_version():
- if sys.version[0:3] not in options_storage.SUPPORTED_PYTHON_VERSIONS:
-@@ -75,8 +91,14 @@
+ def __next_version(version):
+@@ -101,8 +117,14 @@
for binary in ["hammer", "ionhammer", "spades", "bwa-spades", "dipspades"]:
binary_path = os.path.join(binary_dir, binary)
if not os.path.isfile(binary_path):
@@ -55,8 +55,8 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
def check_file_existence(input_filename, message="", log=None, dipspades=False):
filename = abspath(expanduser(input_filename))
---- spades.orig/spades.py
-+++ spades/spades.py
+--- a/spades.py
++++ b/spades.py
@@ -156,6 +156,22 @@
print_value(cfg, "common", "max_memory", "Memory limit (in Gb)", " ")
log.info("")
@@ -80,7 +80,7 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
def fill_cfg(options_to_parse, log, secondary_filling=False):
skip_output_dir=secondary_filling
-@@ -470,7 +486,11 @@
+@@ -502,7 +518,11 @@
if (not options_storage.only_error_correction) and options_storage.mismatch_corrector:
cfg["mismatch_corrector"] = empty_config()
cfg["mismatch_corrector"].__dict__["skip-masked"] = None
diff --git a/debian/patches/0111_use_full_config_dirs.patch b/debian/patches/0111_use_full_config_dirs.patch
index 5524172..21bf6fd 100644
--- a/debian/patches/0111_use_full_config_dirs.patch
+++ b/debian/patches/0111_use_full_config_dirs.patch
@@ -2,9 +2,9 @@ Description: use full config include path
This patch makes sure that the config files are not dependent on local
directory structure.
Author: Sascha Steinbiss <satta at debian.org>
---- spades.orig/src/spades_pipeline/spades_logic.py
-+++ spades/src/spades_pipeline/spades_logic.py
-@@ -185,6 +185,20 @@
+--- a/src/spades_pipeline/spades_logic.py
++++ b/src/spades_pipeline/spades_logic.py
+@@ -209,6 +209,20 @@
add_configs(command, dst_configs)
@@ -25,7 +25,7 @@ Author: Sascha Steinbiss <satta at debian.org>
#print("Calling: " + " ".join(command))
support.sys_call(command, log)
-@@ -232,6 +246,19 @@
+@@ -256,6 +270,19 @@
command = [os.path.join(execution_home, "scaffold_correction"), cfg_file_name]
add_configs(command, dst_configs)
log.info(str(command))
diff --git a/debian/patches/0114_use_debian_provided_libs.patch b/debian/patches/0114_use_debian_provided_libs.patch
index c48b267..33a3f70 100644
--- a/debian/patches/0114_use_debian_provided_libs.patch
+++ b/debian/patches/0114_use_debian_provided_libs.patch
@@ -8,8 +8,8 @@ Description: use Debian-packaged jemalloc library
does not report the 'stats.cactive_max' mallctl stat anymore.
Hence to avoid a NULL dereference the max rss value is logged.
Author: Sascha Steinbiss <satta at debian.org>
---- spades.orig/src/cmake/includes.cmake
-+++ spades/src/cmake/includes.cmake
+--- a/src/cmake/includes.cmake
++++ b/src/cmake/includes.cmake
@@ -3,6 +3,8 @@
set(CMAKE_INCLUDE_CURRENT_DIR ON)
set(CMAKE_INCLUDE_SYSTEM_FLAG_C "-isystem ")
@@ -19,8 +19,8 @@ Author: Sascha Steinbiss <satta at debian.org>
include_directories(${SPADES_MAIN_INCLUDE_DIR} ${SPADES_BUILT_INCLUDE_DIR} ${CMAKE_SOURCE_DIR} ${SPADES_MODULES_DIR})
include_directories(SYSTEM "${EXT_DIR}/include")
include_directories(SYSTEM "${ZLIB_INCLUDE_DIRS}")
---- spades.orig/src/cmake/flags.cmake
-+++ spades/src/cmake/flags.cmake
+--- a/src/cmake/flags.cmake
++++ b/src/cmake/flags.cmake
@@ -53,3 +53,5 @@
if (SPADES_USE_TCMALLOC)
add_compile_options(-fno-omit-frame-pointer)
@@ -28,16 +28,16 @@ Author: Sascha Steinbiss <satta at debian.org>
+
+add_definitions(-DJEMALLOC_NO_DEMANGLE)
\ No newline at end of file
---- spades.orig/src/common/assembly_graph/CMakeLists.txt
-+++ spades/src/common/assembly_graph/CMakeLists.txt
+--- a/src/common/assembly_graph/CMakeLists.txt
++++ b/src/common/assembly_graph/CMakeLists.txt
@@ -9,4 +9,4 @@
add_library(assembly_graph STATIC
components/connected_component.cpp paths/bidirectional_path.cpp paths/bidirectional_path_io/io_support.cpp paths/bidirectional_path_io/bidirectional_path_output.cpp graph_support/scaff_supplementary.cpp ../modules/alignment/edge_index_refiller.cpp graph_support/coverage_uniformity_analyzer.cpp)
-target_link_libraries(assembly_graph hattrie)
+target_link_libraries(assembly_graph hat-trie)
---- spades.orig/src/common/modules/alignment/kmer_map.hpp
-+++ spades/src/common/modules/alignment/kmer_map.hpp
+--- a/src/common/modules/alignment/kmer_map.hpp
++++ b/src/common/modules/alignment/kmer_map.hpp
@@ -9,7 +9,7 @@
#include "sequence/rtseq.hpp"
@@ -47,30 +47,19 @@ Author: Sascha Steinbiss <satta at debian.org>
#include <boost/iterator/iterator_facade.hpp>
namespace debruijn_graph {
---- spades.orig/src/common/modules/path_extend/overlap_analysis.hpp
-+++ spades/src/common/modules/path_extend/overlap_analysis.hpp
+--- a/src/common/modules/path_extend/overlap_analysis.hpp
++++ b/src/common/modules/path_extend/overlap_analysis.hpp
@@ -2,7 +2,7 @@
#include "utils/logger/logger.hpp"
- #include "utils/range.hpp"
+ #include "sequence/range.hpp"
-#include "ssw/ssw_cpp.h"
+#include "ssw_cpp.h"
namespace debruijn_graph {
- using omnigraph::Range;
---- spades.orig/src/common/utils/coverage_model/kmer_coverage_model.cpp
-+++ spades/src/common/utils/coverage_model/kmer_coverage_model.cpp
-@@ -18,7 +18,7 @@
- #include <boost/math/distributions/geometric.hpp>
- #include <boost/math/distributions/pareto.hpp>
--#include <nlopt/nlopt.hpp>
-+#include <nlopt.hpp>
-
- #include <vector>
-
---- spades.orig/src/common/utils/logger/logger_impl.cpp
-+++ spades/src/common/utils/logger/logger_impl.cpp
+--- a/src/common/utils/logger/logger_impl.cpp
++++ b/src/common/utils/logger/logger_impl.cpp
@@ -13,6 +13,7 @@
#include <vector>
@@ -79,105 +68,24 @@ Author: Sascha Steinbiss <satta at debian.org>
#include "config.hpp"
-@@ -101,14 +102,15 @@
+@@ -104,11 +105,12 @@
+ size_t max_rss;
- void logger::log(level desired_level, const char* file, size_t line_num, const char* source, const char* msg) {
- double time = timer_.time();
+ #ifdef SPADES_USE_JEMALLOC
- const size_t *cmem = 0, *cmem_max = 0;
- size_t clen = sizeof(cmem);
+ const size_t *cmem = 0;
-+ size_t clen = sizeof(cmem), cmem_max = 0;
++ size_t clen = sizeof(cmem), *cmem_max = 0;
je_mallctl("stats.cactive", &cmem, &clen, NULL, 0);
- je_mallctl("stats.cactive_max", &cmem_max, &clen, NULL, 0);
+ //je_mallctl("stats.cactive_max", &cmem_max, &clen, NULL, 0);
+ cmem_max = get_max_rss();
-
- for (auto it = writers_.begin(); it != writers_.end(); ++it)
-- (*it)->write_msg(time, (*cmem) / 1024, (*cmem_max) / 1024, desired_level, file, line_num, source, msg);
-+ (*it)->write_msg(time, (*cmem) / 1024, cmem_max, desired_level, file, line_num, source, msg);
- }
+ mem = (*cmem) / 1024;
+ max_rss = (*cmem_max) / 1024;
#else
- void logger::log(level desired_level, const char* file, size_t line_num, const char* source, const char* msg) {
---- spades.orig/src/common/utils/memory_limit.hpp
-+++ spades/src/common/utils/memory_limit.hpp
-@@ -20,6 +20,7 @@
- #include <sys/resource.h>
-
- #include "config.hpp"
-+#include "verify.hpp"
-
- #ifdef SPADES_USE_JEMALLOC
-
---- spades.orig/src/projects/cclean/brute_force_clean.cpp
-+++ spades/src/projects/cclean/brute_force_clean.cpp
-@@ -12,7 +12,7 @@
- #include <iostream>
-
- #include "adapter_index.hpp"
--#include <ssw/ssw_cpp.h> // Striped Smith-Waterman aligner
-+#include "ssw_cpp.h" // Striped Smith-Waterman aligner
- #include "additional.cpp"
- #include "output.hpp"
-
---- spades.orig/src/projects/cclean/job_wrappers.cpp
-+++ spades/src/projects/cclean/job_wrappers.cpp
-@@ -13,7 +13,7 @@
- #include "valid_kmer_generator.hpp"
- #include "adapter_index.hpp"
- #include "output.hpp"
--#include "ssw/ssw_cpp.h"
-+#include "ssw_cpp.h"
- #include "utils.hpp"
-
- using cclean_output::print_alignment;
---- spades.orig/src/projects/cclean/main.cpp
-+++ spades/src/projects/cclean/main.cpp
-@@ -21,7 +21,7 @@
-
- #include "valid_kmer_generator.hpp"
- #include "io/read_processor.hpp"
--#include "modules/ssw_cpp.h"
-+#include "ssw_cpp.h"
- #include "additional.cpp"
-
- #include "job_wrappers.hpp"
---- spades.orig/src/projects/cclean/output.hpp
-+++ spades/src/projects/cclean/output.hpp
-@@ -14,7 +14,7 @@
- #include <io/read.hpp>
- #include <ostream>
- #include "comparator.hpp"
--#include "modules/ssw_cpp.h"
-+#include "ssw_cpp.h"
-
- namespace cclean_output {
-
---- spades.orig/src/projects/cclean/utils.cpp
-+++ spades/src/projects/cclean/utils.cpp
-@@ -12,8 +12,7 @@
- #include <vector>
-
- #include "utils.hpp"
--#include <ssw/ssw_cpp.h>
--#include <ssw/ssw_cpp.h> // Striped Smith-Waterman aligner
-+#include <ssw_cpp.h> // Striped Smith-Waterman aligner
- #include <io/read.hpp>
- #include "additional.cpp"
-
---- spades.orig/src/projects/cclean/utils.hpp
-+++ spades/src/projects/cclean/utils.hpp
-@@ -8,7 +8,7 @@
- #ifndef UTILS_HPP
- #define UTILS_HPP
-
--#include <ssw/ssw_cpp.h> // Striped Smith-Waterman aligner
-+#include <ssw_cpp.h> // Striped Smith-Waterman aligner
- #include <io/read.hpp>
- #include "additional.cpp"
- #include "running_modes.hpp"
---- spades.orig/ext/src/CMakeLists.txt
-+++ spades/ext/src/CMakeLists.txt
+--- a/ext/src/CMakeLists.txt
++++ b/ext/src/CMakeLists.txt
@@ -1,13 +1,9 @@
# -*- cmake -*-
diff --git a/debian/patches/gcc7.patch b/debian/patches/gcc7.patch
index 3b00603..9480fd6 100644
--- a/debian/patches/gcc7.patch
+++ b/debian/patches/gcc7.patch
@@ -3,11 +3,11 @@ Author: Sascha Steinbiss <satta at debian.org>
Forwarded: https://github.com/ablab/spades/issues/26
--- a/src/common/utils/segfault_handler.hpp
+++ b/src/common/utils/segfault_handler.hpp
-@@ -12,6 +12,7 @@
- #include "boost/noncopyable.hpp"
+@@ -13,6 +13,7 @@
+ #include <functional>
#include <signal.h>
+#include <functional>
- struct segfault_handler : boost::noncopyable {
- typedef std::function<void()> callback_t;
+ namespace utils {
+
diff --git a/debian/patches/spelling b/debian/patches/spelling
index 3ab5d50..7284fcc 100644
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -1,8 +1,8 @@
From: Michael R. Crusoe <michael.crusoe at gmail.com>
Subject: Spelling fixes
---- spades.orig/manual.html
-+++ spades/manual.html
-@@ -760,7 +760,7 @@
+--- a/manual.html
++++ b/manual.html
+@@ -761,7 +761,7 @@
Make sure that files with right reads are given in the same order as corresponding files with left reads.
<p>
@@ -11,7 +11,7 @@ Subject: Spelling fixes
<pre class="code">
<code>
lib_pe1_left_1.fastq
-@@ -989,7 +989,7 @@
+@@ -990,7 +990,7 @@
</pre>
<p>
@@ -20,7 +20,7 @@ Subject: Spelling fixes
<pre class="code">
<code>
-@@ -1138,7 +1138,7 @@
+@@ -1139,7 +1139,7 @@
</pre>
<p>
@@ -29,8 +29,8 @@ Subject: Spelling fixes
<pre>
<code>
NODE_3_length_237403_cov_243.207_ID_45
---- spades.orig/src/common/assembly_graph/stats/picture_dump.hpp
-+++ spades/src/common/assembly_graph/stats/picture_dump.hpp
+--- a/src/common/assembly_graph/stats/picture_dump.hpp
++++ b/src/common/assembly_graph/stats/picture_dump.hpp
@@ -123,7 +123,7 @@
INFO("Genome mapping results:");
INFO("Covered k+1-mers:" << covered_kp1mers << " of " << (genome_.size() - k_) << " which is "
@@ -40,9 +40,9 @@ Subject: Spelling fixes
INFO("Continuity failtures " << fail);
}
};
---- spades.orig/src/common/modules/alignment/pacbio/pac_index.hpp
-+++ spades/src/common/modules/alignment/pacbio/pac_index.hpp
-@@ -581,7 +581,7 @@
+--- a/src/common/modules/alignment/pacbio/pac_index.hpp
++++ b/src/common/modules/alignment/pacbio/pac_index.hpp
+@@ -593,7 +593,7 @@
|| !IsConsistent(*(iter->second),
*(next_iter->second))) {
if (next_iter != cur_cluster.end()) {
@@ -51,8 +51,8 @@ Subject: Spelling fixes
DEBUG("on "<< iter->second->str(g_));
DEBUG("and " << next_iter->second->str(g_));
}
---- spades.orig/src/projects/dipspades/kmer_gluing/equal_sequence_gluer.hpp
-+++ spades/src/projects/dipspades/kmer_gluing/equal_sequence_gluer.hpp
+--- a/src/projects/dipspades/kmer_gluing/equal_sequence_gluer.hpp
++++ b/src/projects/dipspades/kmer_gluing/equal_sequence_gluer.hpp
@@ -74,9 +74,9 @@
pos2 = graph_.length(edge1) - tmp - 1;
}
@@ -65,8 +65,8 @@ Subject: Spelling fixes
TRACE("New edge1: " << graph_.int_id(split_edges.first) << ", length: " << graph_.length(split_edges.first));
TRACE("New edge2: " << graph_.int_id(split_edges.second) << ", length: " << graph_.length(split_edges.second));
edge1 = split_edges.first;
---- spades.orig/src/projects/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp
-+++ spades/src/projects/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp
+--- a/src/projects/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp
++++ b/src/projects/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp
@@ -74,7 +74,7 @@
auto splitted_bulge = splitter_.SplitBulge(directed_bulge, glue_def_res);
@@ -76,8 +76,8 @@ Subject: Spelling fixes
GlueSplittedBulge(splitted_bulge);
return true;
}
---- spades.orig/src/projects/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp
-+++ spades/src/projects/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp
+--- a/src/projects/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp
++++ b/src/projects/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp
@@ -260,7 +260,7 @@
SplitOppositeEdge(split_res, split_paths.second, split_partlens.second);
--
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