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