[med-svn] [Git][med-team/pbseqlib][upstream] New upstream version 5.3.4+dfsg

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / pbseqlib


Commits:
c95a8587 by Andreas Tille at 2020-11-13T08:56:25+01:00
New upstream version 5.3.4+dfsg
- - - - -


5 changed files:

- alignment/query/PbiFilterZmwGroupQuery.cpp
- bamboo_build.sh
- meson.build
- + subprojects/htslib.wrap
- + subprojects/zlib.wrap


Changes:

=====================================
alignment/query/PbiFilterZmwGroupQuery.cpp
=====================================
@@ -19,7 +19,7 @@ struct PbiFilterZmwGroupQuery::PbiFilterZmwGroupQueryPrivate
     /// sequentially in bam files, such as in movie.subreads.bam.
 public:
     PbiFilterZmwGroupQueryPrivate(const PbiFilter& filter, const DataSet& dataset)
-        : reader_(new PbiFilterCompositeBamReader<Compare::None>(filter, dataset))
+        : reader_(new PbiFilterCompositeBamReader<Compare::Zmw>(filter, dataset))
         , nextRecord_(boost::none)
     {
     }
@@ -59,7 +59,7 @@ public:
     }
 
 public:
-    std::unique_ptr<PbiFilterCompositeBamReader<Compare::None>> reader_;
+    std::unique_ptr<PbiFilterCompositeBamReader<Compare::Zmw>> reader_;
 
     boost::optional<BamRecord> nextRecord_;
 };


=====================================
bamboo_build.sh
=====================================
@@ -67,7 +67,7 @@ for i in "1.10" "1.8"; do
   # 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


=====================================
meson.build
=====================================
@@ -1,11 +1,11 @@
 project(
   'libblasr',
   'cpp',
-  version : '5.3.3',
+  version : '5.3.4',
   default_options : [
     'buildtype=release',
     'warning_level=3',
-    'cpp_std=c++11',
+    'cpp_std=c++14',
     'b_ndebug=false'],
   license : 'BSD-3',
   meson_version : '>= 0.46.0')
@@ -52,12 +52,20 @@ libblasr_boost_dep = dependency('boost', required : true)
 libblasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])
 
 # zlib
-libblasr_zlib_dep = dependency('zlib', required : true)
+libblasr_zlib_dep = dependency('zlib', required : true, fallback : ['zlib', 'zlib_dep'])
+
+# htslib
+libblasr_htslib_dep = dependency('htslib', required : true, version : '>=1.4', fallback : ['htslib', 'htslib_dep'])
 
 # clock_gettime on old glibc systems
 libblasr_rt_dep = cpp.find_library('rt', required : false)
 
-libblasr_deps = [libblasr_boost_dep, libblasr_pbbam_dep, libblasr_zlib_dep, libblasr_rt_dep]
+libblasr_deps = [
+  libblasr_boost_dep,
+  libblasr_pbbam_dep,
+  libblasr_zlib_dep,
+  libblasr_htslib_dep,
+  libblasr_rt_dep]
 
 ##########
 # Config #


=====================================
subprojects/htslib.wrap
=====================================
@@ -0,0 +1,10 @@
+[wrap-file]
+directory = htslib-1.9
+
+source_url = https://github.com/samtools/htslib/archive/1.9.zip
+source_filename = htslib-1.9.zip
+source_hash = c4d3ae84014f8a80f5011521f391e917bc3b4f6ebd78e97f238472e95849ec14
+
+patch_url = https://wrapdb.mesonbuild.com/v1/projects/htslib/1.9/1/get_zip
+patch_filename = htslib-1.9-1-wrap.zip
+patch_hash = 02f4a3c64d668d4d09f8bb0f57eb33398e90e6901989f257be6a6716a15bdcdd


=====================================
subprojects/zlib.wrap
=====================================
@@ -0,0 +1,10 @@
+[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/1.2.11/4/get_zip
+patch_filename = zlib-1.2.11-4-wrap.zip
+patch_hash = f733976fbfc59e0bcde01aa9469a24eeb16faf0a4280b17e9eaa60a301d75657



View it on GitLab: https://salsa.debian.org/med-team/pbseqlib/-/commit/c95a85872d52ff61bcbc40950abebf023b3a4798

-- 
View it on GitLab: https://salsa.debian.org/med-team/pbseqlib/-/commit/c95a85872d52ff61bcbc40950abebf023b3a4798
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