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Author: Andreas Tille <tille@debian.org>
Last-update: Sat, 10 Sep 2016 23:41:37 +0200
Description: Use Debian packaged libgzstream
--- a/configure.ac
+++ b/configure.ac
@@ -376,7 +376,6 @@ AC_CONFIG_FILES([\
control crac.spec \
Makefile src/Makefile scripts/Makefile \
src/libReadsInfo/Makefile src/libSSA/Makefile \
- src/libgzstream/Makefile \
src/libReadsReader/Makefile \
src/libReadsReader/kseq/Makefile \
man/Makefile man/crac.1 \
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -107,7 +107,7 @@ CRAC_LINKS = crac-index
all-local: $(bin_PROGRAMS) $(CRAC_LINKS)
-SUBDIRS = libReadsInfo libSSA libgzstream libReadsReader
+SUBDIRS = libReadsInfo libSSA libReadsReader
if INCLUDED_GKARRAYS
SUBDIRS += libGkArrays
endif
@@ -133,7 +133,7 @@ crac_SOURCES = \
locateServer.cpp locateServer.h \
utils.cpp utils.h \
Bitset.cpp Bitset.h
-crac_LDADD = @abs_builddir@/libSSA/libSSA.a @abs_builddir@/libReadsInfo/libReadsInfo.a @abs_builddir@/libgzstream/libgzstream.a @abs_builddir@/libReadsReader/libReadsReader.a
+crac_LDADD = @abs_builddir@/libSSA/libSSA.a @abs_builddir@/libReadsInfo/libReadsInfo.a @abs_builddir@/libReadsReader/libReadsReader.a
#crac_index_SOURCES = @abs_srcdir@/libSSA/cracIndex.cpp
#crac_index_LDADD = @abs_builddir@/libSSA/libSSA.a
@@ -145,8 +145,8 @@ crac-emt: @abs_builddir@/libSSA/crac-emt
$(LN_S) -f $^ $@
-AM_LDFLAGS = -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L@abs_builddir@/libSSA -L@abs_builddir@/libReadsInfo -L@abs_builddir@/libgzstream -L@abs_builddir@/libReadsReader #-pg # for Gprof
-AM_CPPFLAGS = -I@abs_top_srcdir@ -I@abs_srcdir@ -I@abs_srcdir@/libSSA -I@abs_srcdir@/libSSA/karkkainen_bwt -I@abs_srcdir@/libgzstream
+AM_LDFLAGS = -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L@abs_builddir@/libSSA -L@abs_builddir@/libReadsInfo -L@abs_builddir@/libReadsReader #-pg # for Gprof
+AM_CPPFLAGS = -I@abs_top_srcdir@ -I@abs_srcdir@ -I@abs_srcdir@/libSSA -I@abs_srcdir@/libSSA/karkkainen_bw
if INCLUDED_JELLYFISH
AM_LDFLAGS += -L@abs_builddir@/libJellyfish-2.0/.libs
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