[med-svn] [Git][med-team/blasr][upstream] New upstream version 5.3.5+dfsg

[Andreas Tille (@tille)]

Andreas Tille pushed to branch upstream at Debian Med / blasr


Commits:
c2755bbb by Andreas Tille at 2021-10-08T16:07:31+02:00
New upstream version 5.3.5+dfsg
- - - - -


9 changed files:

- .gitignore
- Blasr.cpp
- bamboo_build.sh
- ctest/meson.build
- iblasr/BlasrUtilsImpl.hpp
- meson.build
- + subprojects/htslib.wrap
- + subprojects/pbcopper.wrap
- + subprojects/zlib.wrap


Changes:

=====================================
.gitignore
=====================================
@@ -14,6 +14,5 @@ build/
 /utils/bax2bam/tests/src/TestData.h
 
 # Meson WrapDB stuff
-subprojects/packagecache/
-subprojects/blasr_libcpp*
-subprojects/pbbam*
+/subprojects/*
+!/subprojects/*.wrap


=====================================
Blasr.cpp
=====================================
@@ -1459,7 +1459,7 @@ int main(int argc, char *argv[])
                 }
                 delete bamWriterPtr;
                 bamWriterPtr = NULL;
-            } catch (std::exception e) {
+            } catch (const std::exception &e) {
                 std::cout << "Error, could not flush bam records to bam file." << std::endl;
                 std::exit(EXIT_FAILURE);
             }


=====================================
bamboo_build.sh
=====================================
@@ -64,7 +64,7 @@ export ENABLED_TESTS="true"
 # TODO(dseifert)
 # HDF5 doesn't have pkg-config files yet
 export CPPFLAGS="${HDF5_CFLAGS}"
-export LDFLAGS="-static-libstdc++ -static-libgcc ${HDF5_LIBS}"
+export LDFLAGS="-static-libstdc++ -static-libgcc ${HDF5_LIBS} -Wl,-rpath-link,${LD_LIBRARY_PATH}"
 
 bash scripts/ci/build.sh
 bash scripts/ci/test.sh


=====================================
ctest/meson.build
=====================================
@@ -41,7 +41,7 @@ blasr_test_outdir = join_paths(blasr_test_testdir, 'out')
 
 foreach i : blasr_fast_test_list
   test(
-    'blasr *' + i[1] + '* cram test: "' + i[0] + '"',
+    'blasr cram test - ' + i[0],
     blasr_cram_script,
     args : [
       '--xunit-file=' + join_paths(meson.build_root(), 'blasr-cram-' + i[0] + '.xml'),


=====================================
iblasr/BlasrUtilsImpl.hpp
=====================================
@@ -973,7 +973,7 @@ void PrintAlignment(T_AlignmentCandidate &alignment, SMRTSequence &fullRead,
                 SummaryOutput::Print(alignment, outFile);
             }
         }
-    } catch (std::ostream::failure f) {
+    } catch (const std::ostream::failure &f) {
         std::cout << "ERROR writing to output file. The output drive may be full, or you  "
                   << std::endl;
         std::cout << "may not have proper write permissions." << std::endl;


=====================================
meson.build
=====================================
@@ -1,14 +1,14 @@
 project(
   'blasr',
   'cpp',
-  version : '5.3.3',
+  version : '5.3.5',
   default_options : [
     'buildtype=release',
     'warning_level=3',
-    'cpp_std=c++11',
+    'cpp_std=c++17',
     'b_ndebug=false'],
   license : 'BSD-3',
-  meson_version : '>= 0.46.0')
+  meson_version : '>= 0.52.0')
 
 # TODO:
 # try to reenable 'b_ndebug=true'
@@ -48,7 +48,7 @@ endif
 blasr_thread_dep = dependency('threads', required : true)
 
 # boost
-blasr_boost_dep = dependency('boost', required : true)
+blasr_boost_dep = dependency('boost', include_type : 'system', required : true)
 
 # pbbam
 blasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])
@@ -57,9 +57,18 @@ blasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])
 blasr_libblasr_dep = dependency('libblasr', fallback : ['blasr_libcpp', 'libblasr_dep'])
 
 # zlib
-blasr_zlib_dep = dependency('zlib', required : true)
-
-blasr_deps = [blasr_thread_dep, blasr_boost_dep, blasr_pbbam_dep, blasr_libblasr_dep, blasr_zlib_dep]
+blasr_zlib_dep = dependency('zlib', required : true, fallback : ['zlib', 'zlib_dep'])
+
+# htslib
+blasr_htslib_dep = dependency('htslib', required : true, version : '>=1.4', fallback : ['htslib', 'htslib_dep'])
+
+blasr_deps = [
+  blasr_thread_dep,
+  blasr_boost_dep,
+  blasr_pbbam_dep,
+  blasr_libblasr_dep,
+  blasr_zlib_dep,
+  blasr_htslib_dep]
 
 ########################
 # sources + executable #


=====================================
subprojects/htslib.wrap
=====================================
@@ -0,0 +1,12 @@
+[wrap-file]
+directory = htslib-1.10.2
+source_url = https://github.com/samtools/htslib/archive/1.10.2.zip
+source_filename = htslib-1.10.2.zip
+source_hash = f7994e9636f8a4032dea477a8613f5f73b330c23b5538e45666ce7306240ac14
+patch_url = https://wrapdb.mesonbuild.com/v1/projects/htslib/1.10.2/1/get_zip
+patch_filename = htslib-1.10.2-1-wrap.zip
+patch_hash = 7e8a0bfef2fb17e78ba1a8fd78e152bfbcfcb941b555d88c75b6d818a07d49d1
+
+[provide]
+htslib = htslib_dep
+


=====================================
subprojects/pbcopper.wrap
=====================================
@@ -0,0 +1,4 @@
+[wrap-git]
+directory=pbcopper
+url=https://github.com/PacificBiosciences/pbcopper.git
+revision=develop


=====================================
subprojects/zlib.wrap
=====================================
@@ -0,0 +1,12 @@
+[wrap-file]
+directory = zlib-1.2.11
+source_url = http://zlib.net/fossils/zlib-1.2.11.tar.gz
+source_filename = zlib-1.2.11.tar.gz
+source_hash = c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1
+patch_url = https://wrapdb.mesonbuild.com/v1/projects/zlib/1.2.11/5/get_zip
+patch_filename = zlib-1.2.11-5-wrap.zip
+patch_hash = 728c8e24acbc2e6682fbd950fec39e2fc77528af361adb87259f8a8511434004
+
+[provide]
+zlib = zlib_dep
+



View it on GitLab: https://salsa.debian.org/med-team/blasr/-/commit/c2755bbb5fe03cf90b30a0097235de4fd634ef53

-- 
View it on GitLab: https://salsa.debian.org/med-team/blasr/-/commit/c2755bbb5fe03cf90b30a0097235de4fd634ef53
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