Author: Andreas Tille <tille@debian.org>
Last-update: Sat, 10 Sep 2016 23:41:37 +0200
Description: Use Debian packaged libgtkarrays

--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -108,9 +108,6 @@ all-local: $(bin_PROGRAMS) $(CRAC_LINKS)
 
 
 SUBDIRS = libReadsInfo libSSA libReadsReader
-if INCLUDED_GKARRAYS
-  SUBDIRS += libGkArrays
-endif
 
 crac_SOURCES =                    \
   basic.h const.h types.h         \
@@ -152,11 +149,11 @@ if INCLUDED_JELLYFISH
 endif
 
 if INCLUDED_GKARRAYS
-  AM_LDFLAGS += -L@abs_builddir@/libGkArrays/src/.libs
-  AM_CPPFLAGS += -I@abs_srcdir@/libGkArrays/src/
+  AM_LDFLAGS += `pkg-config --libs libGkArrays`
+  AM_CPPFLAGS += `pkg-config --cflags libGkArrays`
 if INCLUDED_PROGRESSBAR
-  AM_LDFLAGS += -L@abs_builddir@/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar
-  AM_CPPFLAGS += -I@abs_srcdir@/libGkArrays/src/libProgressBar-1.2.0/
+  AM_LDFLAGS += `pkg-config --libs libProgressBar`
+  AM_CPPFLAGS += `pkg-config --cflags libProgressBar`
 endif
 endif
 
--- a/src/libReadsInfo/Makefile.am
+++ b/src/libReadsInfo/Makefile.am
@@ -124,7 +124,7 @@ libReadsInfo_a_SOURCES =
 
 libReadsInfo_a_CPPFLAGS = -I@abs_top_srcdir@ -I@abs_top_srcdir@/src -I@abs_top_srcdir@/src/libSSA 
 if INCLUDED_GKARRAYS
-  libReadsInfo_a_CPPFLAGS += -I@abs_srcdir@/../libGkArrays/src/
+  libReadsInfo_a_CPPFLAGS += `pkg-config --cflags libGkArrays`
 endif
 
 
--- a/src/libSSA/Makefile.am
+++ b/src/libSSA/Makefile.am
@@ -101,7 +101,7 @@
 bin_PROGRAMS = crac-index
 crac_index_SOURCES = cracIndex.cpp cracIndex.h
 
-AM_CPPFLAGS = -I@abs_top_srcdir@ -I@abs_srcdir@/karkkainen_bwt -I@abs_top_srcdir@/src/libGkArrays/src
+AM_CPPFLAGS = -I@abs_top_srcdir@ -I@abs_srcdir@/karkkainen_bwt `pkg-config --cflags libGkArrays`
 AM_LDFLAGS = -lm -lpthread -lSSA -L@abs_builddir@/
 LDADD = libSSA.a