debian/changelog

@@ -13,4 +13,13 @@ sailfish (0.10.1+dfsg-1) UNRELEASED; urgency=medium
         
             Updated fmt lib to version 0d5ef5c2a66026409b0cfbafa1d2f46cdc5aa4d0
     
+    2. Rapmap version conflict with the Debian packaged rapmap-dev:
+        In file included from /usr/include/rapmap/RapMapUtils.hpp:32,
+                        from /usr/include/rapmap/RapMapSAIndex.hpp:44,
+                        from /build/sailfish-0.10.1+dfsg/src/SailfishIndexer.cpp:60:
+        /usr/include/rapmap/Kmer.hpp:138:77: error: macro "bitmask" requires 2 arguments, but only 1 given
+         template <typename R> static constexpr R bitmask(unsigned int const onecount) {
+                                                                                     ^
+
+
  -- Steffen Moeller <moeller@debian.org>  Thu, 21 Mar 2019 22:47:18 +0100

debian/control

@@ -21,7 +21,8 @@ Build-Depends: debhelper (>= 12),
                libsparsehash-dev,
                libeigen3-dev,
                libspdlog-dev,
-               libcereal-dev
+               libcereal-dev,
+               rapmap-dev
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/sailfish
 Vcs-Git: https://salsa.debian.org/med-team/sailfish.git

debian/patches/dfsg-please.patch

@@ -115,7 +115,7 @@ Description: Make sure we build against Debian packaged libraries
  
 --- a/src/CMakeLists.txt
 +++ b/src/CMakeLists.txt
-@@ -24,23 +24,23 @@ EmpiricalDistribution.cpp
+@@ -24,26 +24,23 @@ EmpiricalDistribution.cpp
  #HDF5Writer.cpp
  GZipWriter.cpp
  xxhash.c
@@ -141,10 +141,14 @@ Description: Make sure we build against Debian packaged libraries
  ${GAT_SOURCE_DIR}/tests
  ${GAT_SOURCE_DIR}/include
 -${GAT_SOURCE_DIR}/include/eigen3
-+/usr/include/eigen3
- ${GAT_SOURCE_DIR}/external
+-${GAT_SOURCE_DIR}/external
 -${GAT_SOURCE_DIR}/external/cereal/include
+-${GAT_SOURCE_DIR}/external/install/include
+-${GAT_SOURCE_DIR}/external/install/include/rapmap
+-${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.2.3
++/usr/include/eigen3
 +/usr/include/cereal
- ${GAT_SOURCE_DIR}/external/install/include
- ${GAT_SOURCE_DIR}/external/install/include/rapmap
- ${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.2.3
++/usr/include/rapmap
+ ${ZLIB_INCLUDE_DIR}
+ ${TBB_INCLUDE_DIRS}
+ ${Boost_INCLUDE_DIRS}