kallisto: Rebundle htslib

Bundled, outdated htslib is not compatible with latest
Modified bits of htslib code are sprinkled around kallisto src like a cancer

diff --git a/kallisto/patches/patch-CMakeLists.txt b/kallisto/patches/patch-CMakeLists.txt
deleted file mode 100644 (file)
index 0bd8d40..0000000
--- a/kallisto/patches/patch-CMakeLists.txt
+++ /dev/null
@@ -1,28 +0,0 @@
-$NetBSD: patch-CMakeLists.txt,v 1.1 2018/12/21 19:00:56 bacon Exp $
-
-# Unbundle htslib
-
---- CMakeLists.txt.orig        2018-12-19 17:13:04.000000000 +0000
-+++ CMakeLists.txt
-@@ -35,21 +35,6 @@ ELSE(LINK MATCHES shared)
- ENDIF(LINK MATCHES static)
- 
- 
--include(ExternalProject)
--ExternalProject_Add(htslib
--    PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
--    SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
--    BUILD_IN_SOURCE 1
--    CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure 
--        --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
--    BUILD_COMMAND make lib-static
--    INSTALL_COMMAND ""
--)
--
--include_directories(${htslib_PREFIX}/src/htslib)
--
--
--
- # add_compile_options(-Wdeprecated-register)
- 
- add_subdirectory(src)

diff --git a/kallisto/patches/patch-src_CMakeLists.txt b/kallisto/patches/patch-src_CMakeLists.txt
deleted file mode 100644 (file)
index bbc8df4..0000000
--- a/kallisto/patches/patch-src_CMakeLists.txt
+++ /dev/null
@@ -1,30 +0,0 @@
-$NetBSD: patch-src_CMakeLists.txt,v 1.1 2018/12/21 19:00:56 bacon Exp $
-
-# Unbundle htslib
-
---- src/CMakeLists.txt.orig    2018-10-17 23:58:22 UTC
-+++ src/CMakeLists.txt
-@@ -3,15 +3,13 @@ file(GLOB headers *.h *.hpp)
- 
- list(REMOVE_ITEM sources main.cpp)
- 
--include_directories(../ext/htslib)
--
- add_library(kallisto_core ${sources} ${headers})
- target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
- 
- add_executable(kallisto main.cpp)
- 
- find_package( Threads REQUIRED )
--target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
-+target_link_libraries(kallisto kallisto_core pthread hts)
- 
- if(LINK MATCHES static)
-     set(BUILD_SHARED_LIBS OFF)
-@@ -56,4 +54,4 @@ else()
- endif(LINK MATCHES static)
- 
- 
--install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
-\ No newline at end of file
-+install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")