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Author: Andreas Tille <tille@debian.org>
Last-Update: 2021-01-28
Description: Use Debian packaged libsmithwaterman
Forwarded: not-needed
--- libvcflib.orig/CMakeLists.txt
+++ libvcflib/CMakeLists.txt
@@ -59,6 +59,7 @@
pkg_check_modules(HTSLIB htslib) # Optionally builds from contrib/
pkg_check_modules(TABIXPP tabixpp) # Optionally builds from contrib/
+pkg_check_modules(SMITHWATERMAN REQUIRED IMPORTED_TARGET libsmithwaterman)
# ---- Build switches
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
@@ -110,7 +111,6 @@
include_directories(include)
include_directories(contrib/fastahack)
include_directories(contrib/intervaltree)
-include_directories(contrib/smithwaterman)
# include_directories(contrib/multichoose) merged with vcflib
include_directories(contrib/filevercmp)
include_directories(contrib/c-progress-bar)
@@ -146,7 +146,6 @@
src/*.h*
# contrib/multichoose/*.h*
contrib/intervaltree/*.h*
- contrib/smithwaterman/*.h*
contrib/fastahack/*.h*
contrib/filevercmp/*.h*
)
@@ -172,15 +171,14 @@
src/cigar.cpp
src/allele.cpp
contrib/fastahack/Fasta.cpp
- contrib/smithwaterman/SmithWatermanGotoh.cpp
- contrib/smithwaterman/Repeats.cpp
- contrib/smithwaterman/IndelAllele.cpp
- contrib/smithwaterman/disorder.cpp
- contrib/smithwaterman/LeftAlign.cpp
contrib/filevercmp/filevercmp.c
contrib/c-progress-bar/progress.c
)
+target_link_libraries(vcflib
+ PkgConfig::SMITHWATERMAN
+ )
+
if (TABIXPP_LOCAL) # add the tabixpp source file
list(APPEND vcflib_SOURCE ${tabixpp_SOURCE})
endif()
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