debian/changelog

-spoa (3.0.0-1) UNRELEASED; urgency=medium
+spoa (3.0.0-1) unstable; urgency=medium
 
   * New upstream version
   * Standards-Version: 4.4.0
-  TODO: Newer version of libbioparser-dev (see
-        https://github.com/rvaser/bioparser/issues/4 )
+  * Versioned Build-Depends: libbioparser-dev (>= 2.0)
+  * Bump soversion to 3
 
- -- Andreas Tille <tille@debian.org>  Fri, 12 Jul 2019 21:06:20 +0200
+ -- Andreas Tille <tille@debian.org>  Mon, 15 Jul 2019 16:12:17 +0200
 
 spoa (1.1.5-1) unstable; urgency=medium
 

debian/control

@@ -7,7 +7,7 @@ Build-Depends: debhelper (>= 12~),
                cmake,
                d-shlibs,
                rename,
-               libbioparser-dev,
+               libbioparser-dev (>= 2.0),
                libgtest-dev,
                zlib1g-dev
 Standards-Version: 4.4.0
@@ -27,7 +27,7 @@ Description: SIMD partial order alignment tool
  (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment
  (overlap).
 
-Package: libspoa1.1.5
+Package: libspoa3
 Architecture: amd64
 Section: libs
 Depends: ${shlibs:Depends},
@@ -47,7 +47,7 @@ Architecture: amd64
 Section: libdevel
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         libspoa1.1.5 (= ${binary:Version})
+         libspoa3 (= ${binary:Version})
 Description: SIMD partial order alignment library (development files)
  Spoa (SIMD POA) is a c++ implementation of the partial order alignment
  (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which

debian/libspoa1.1.5.symbols → debian/libspoa3.symbols

-libspoa.so.1.1.5 libspoa1.1.5 #MINVER#
+libspoa.so.3 libspoa3 #MINVER#
  _ZN4spoa11createGraphEv@Base 1.1.3
- _ZN4spoa15AlignmentEngine25align_sequence_with_graphERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt10unique_ptrINS_5GraphESt14default_deleteISA_EE@Base 1.1.3
- _ZN4spoa15AlignmentEngineC1ENS_13AlignmentTypeEaaa@Base 1.1.3
- _ZN4spoa15AlignmentEngineC2ENS_13AlignmentTypeEaaa@Base 1.1.3
- _ZN4spoa19SimdAlignmentEngine25align_sequence_with_graphEPKcjRKSt10unique_ptrINS_5GraphESt14default_deleteIS4_EE@Base 1.1.3
+ _ZN4spoa15AlignmentEngine5alignERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt10unique_ptrINS_5GraphESt14default_deleteISA_EE@Base 3.0.0
+ _ZN4spoa15AlignmentEngineC1ENS_13AlignmentTypeENS_16AlignmentSubtypeEaaaaaa@Base 3.0.0
+ _ZN4spoa15AlignmentEngineC2ENS_13AlignmentTypeENS_16AlignmentSubtypeEaaaaaa@Base 3.0.0
+ _ZN4spoa19SimdAlignmentEngine5alignEPKcjRKSt10unique_ptrINS_5GraphESt14default_deleteIS4_EE@Base 3.0.0
  _ZN4spoa19SimdAlignmentEngine7reallocEjjj@Base 1.1.3
  _ZN4spoa19SimdAlignmentEngine8preallocEjj@Base 1.1.3
- _ZN4spoa19SimdAlignmentEngineC1ENS_13AlignmentTypeEaaa@Base 1.1.3
- _ZN4spoa19SimdAlignmentEngineC2ENS_13AlignmentTypeEaaa@Base 1.1.3
+ _ZN4spoa19SimdAlignmentEngineC1ENS_13AlignmentTypeENS_16AlignmentSubtypeEaaaaaa@Base 3.0.0
+ _ZN4spoa19SimdAlignmentEngineC2ENS_13AlignmentTypeENS_16AlignmentSubtypeEaaaaaa@Base 3.0.0
  _ZN4spoa19SimdAlignmentEngineD0Ev@Base 1.1.3
  _ZN4spoa19SimdAlignmentEngineD1Ev@Base 1.1.3
  _ZN4spoa19SimdAlignmentEngineD2Ev@Base 1.1.3
  _ZN4spoa19SisdAlignmentEngine10initializeEPKcjRKSt10unique_ptrINS_5GraphESt14default_deleteIS4_EE@Base 1.1.3
- _ZN4spoa19SisdAlignmentEngine25align_sequence_with_graphEPKcjRKSt10unique_ptrINS_5GraphESt14default_deleteIS4_EE@Base 1.1.3
  _ZN4spoa19SisdAlignmentEngine5alignEPKcjRKSt10unique_ptrINS_5GraphESt14default_deleteIS4_EE@Base 1.1.3
+ _ZN4spoa19SisdAlignmentEngine6affineEPKcjRKSt10unique_ptrINS_5GraphESt14default_deleteIS4_EE@Base 3.0.0
+ _ZN4spoa19SisdAlignmentEngine6convexEPKcjRKSt10unique_ptrINS_5GraphESt14default_deleteIS4_EE@Base 3.0.0
+ _ZN4spoa19SisdAlignmentEngine6linearEPKcjRKSt10unique_ptrINS_5GraphESt14default_deleteIS4_EE@Base 3.0.0
  _ZN4spoa19SisdAlignmentEngine7reallocEjjj@Base 1.1.3
  _ZN4spoa19SisdAlignmentEngine8preallocEjj@Base 1.1.3
- _ZN4spoa19SisdAlignmentEngineC1ENS_13AlignmentTypeEaaa@Base 1.1.3
- _ZN4spoa19SisdAlignmentEngineC2ENS_13AlignmentTypeEaaa@Base 1.1.3
+ _ZN4spoa19SisdAlignmentEngineC1ENS_13AlignmentTypeENS_16AlignmentSubtypeEaaaaaa@Base 3.0.0
+ _ZN4spoa19SisdAlignmentEngineC2ENS_13AlignmentTypeENS_16AlignmentSubtypeEaaaaaa@Base 3.0.0
  _ZN4spoa19SisdAlignmentEngineD0Ev@Base 1.1.3
  _ZN4spoa19SisdAlignmentEngineD1Ev@Base 1.1.3
  _ZN4spoa19SisdAlignmentEngineD2Ev@Base 1.1.3
  _ZN4spoa21createAlignmentEngineENS_13AlignmentTypeEaaa@Base 1.1.3
- _ZN4spoa25createSimdAlignmentEngineENS_13AlignmentTypeEaaa@Base 1.1.3
- _ZN4spoa25createSisdAlignmentEngineENS_13AlignmentTypeEaaa@Base 1.1.3
+ _ZN4spoa21createAlignmentEngineENS_13AlignmentTypeEaaaa@Base 3.0.0
+ _ZN4spoa21createAlignmentEngineENS_13AlignmentTypeEaaaaaa@Base 3.0.0
+ _ZN4spoa25createSimdAlignmentEngineENS_13AlignmentTypeENS_16AlignmentSubtypeEaaaaaa@Base 3.0.0
+ _ZN4spoa25createSisdAlignmentEngineENS_13AlignmentTypeENS_16AlignmentSubtypeEaaaaaa@Base 3.0.0
  _ZN4spoa4Edge12add_sequenceEjj@Base 1.1.3
  _ZN4spoa4EdgeC1Ejjjj@Base 1.1.3
  _ZN4spoa4EdgeC2Ejjjj@Base 1.1.3
@@ -48,6 +52,7 @@ libspoa.so.1.1.5 libspoa1.1.5 #MINVER#
  _ZN4spoa5Graph18generate_consensusB5cxx11Ev@Base 1.1.3
  _ZN4spoa5Graph24traverse_heaviest_bundleEv@Base 1.1.3
  _ZN4spoa5Graph36generate_multiple_sequence_alignmentERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EEb@Base 1.1.3
+ _ZN4spoa5Graph5clearEv@Base 3.0.0
  _ZN4spoa5Graph8add_edgeEjjj@Base 1.1.3
  _ZN4spoa5Graph8add_nodeEj@Base 1.1.3
  _ZN4spoa5GraphC1Ev@Base 1.1.3
@@ -82,7 +87,9 @@ libspoa.so.1.1.5 libspoa1.1.5 #MINVER#
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base 1.1.3
  _ZNSt6vectorISt10shared_ptrIN4spoa4EdgeEESaIS3_EE17_M_realloc_insertIJRS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_@Base 1.1.3
  _ZNSt6vectorISt10unique_ptrIN4spoa4NodeESt14default_deleteIS2_EESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base 1.1.3
- _ZNSt6vectorISt4pairIiiESaIS1_EE17_M_realloc_insertIJjjEEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_@Base 1.1.3
+ _ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJRKjiEEEvDpOT_@Base 3.0.0
+ _ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJijEEEvDpOT_@Base 3.0.0
+ _ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJjjEEEvDpOT_@Base 3.0.0
  _ZNSt6vectorIbSaIbEE14_M_fill_insertESt13_Bit_iteratormb@Base 1.1.3
  _ZNSt6vectorIiSaIiEE14_M_fill_insertEN9__gnu_cxx17__normal_iteratorIPiS1_EEmRKi@Base 1.1.3
  _ZNSt6vectorIjSaIjEE12emplace_backIJRKiEEEvDpOT_@Base 1.1.3

debian/patches/fix_soversion.patch

@@ -6,12 +6,10 @@ Bug-Upstream: https://github.com/rvaser/spoa/issues/14
 
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -41,7 +41,7 @@ target_include_directories(spoa_static P
- set_target_properties(spoa
-     PROPERTIES
-     VERSION ${spoa_VERSION}
--    SOVERSION ${spoa_VERSION})
-+    SOVERSION 2)
+@@ -1,5 +1,5 @@
+ cmake_minimum_required(VERSION 3.2)
+-project(spoa LANGUAGES CXX VERSION 3.0.0)
++project(spoa LANGUAGES CXX VERSION 3)
+ 
+ include(GNUInstallDirs)
  
- install(TARGETS spoa DESTINATION ${CMAKE_INSTALL_LIBDIR})
- install(TARGETS spoa_static DESTINATION ${CMAKE_INSTALL_LIBDIR})

debian/patches/series

 use_debian_packaged_libs.patch
 shared_and_static.patch
-# fix_soversion.patch
+fix_soversion.patch