added lzma and lbz2 flags to build

walaj · Mar 1, 2019 · e91ab4b · e91ab4b
1 parent e9a82f6
commit e91ab4b
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Showing 4 changed files with 6 additions and 4 deletions.
diff --git a/configure b/configure
@@ -4843,7 +4843,7 @@ AM_CXXFLAGS="-g -Wall -Wextra $fail_on_warning -Wno-unknown-pragmas -std=c++11 -
 ##AC_SUBST(CXXFLAGS, "-O3")
 ##AC_SUBST(CFLAGS, "-O3")
 ##AC_SUBST(CPPFLAGS, "$CPPFLAGS $boost_include")
-LDFLAGS="$LDFLAGS -pthread -std=c++11 -lbz2 -llzma"
+LDFLAGS="$LDFLAGS -pthread -std=c++11"
 
 
 # We always need to specify to link to certain libraries

diff --git a/configure.ac b/configure.ac
@@ -45,7 +45,7 @@ AC_SUBST(AM_CXXFLAGS, "-g -Wall -Wextra $fail_on_warning -Wno-unknown-pragmas -s
 ##AC_SUBST(CXXFLAGS, "-O3")
 ##AC_SUBST(CFLAGS, "-O3")
 ##AC_SUBST(CPPFLAGS, "$CPPFLAGS $boost_include")
-AC_SUBST(LDFLAGS, "$LDFLAGS -pthread -std=c++11 -lbz2 -llzma")
+AC_SUBST(LDFLAGS, "$LDFLAGS -pthread -std=c++11")
 
 # We always need to specify to link to certain libraries
 ##AC_SUBST(LIBS, "$LIBS") # libboost_regex.a libboost_filesystem.a libboost_system.a")

diff --git a/src/svaba/Makefile.am b/src/svaba/Makefile.am
@@ -22,7 +22,8 @@ svaba_LDADD = \
 	$(top_builddir)/SeqLib/src/libseqlib.a \
 	$(top_builddir)/SeqLib/bwa/libbwa.a \
 	$(top_builddir)/SeqLib/htslib/libhts.a \
-	$(top_builddir)/SeqLib/fermi-lite/libfml.a
+	$(top_builddir)/SeqLib/fermi-lite/libfml.a \
+	-llzma -lbz2 -lz
 
 ##svaba_LDFLAGS = -pthread -std=c++11
 

diff --git a/src/svaba/Makefile.in b/src/svaba/Makefile.in
@@ -318,7 +318,8 @@ svaba_LDADD = \
 	$(top_builddir)/SeqLib/src/libseqlib.a \
 	$(top_builddir)/SeqLib/bwa/libbwa.a \
 	$(top_builddir)/SeqLib/htslib/libhts.a \
-	$(top_builddir)/SeqLib/fermi-lite/libfml.a
+	$(top_builddir)/SeqLib/fermi-lite/libfml.a \
+	-llzma -lbz2 -lz
 
 svaba_SOURCES = run_svaba.cpp BreakPoint.cpp AlignedContig.cpp AlignmentFragment.cpp \
 		DiscordantCluster.cpp DBSnpFilter.cpp PONFilter.cpp \