Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 27 Jan 2017 13:18:48 +0100
Description: Make sure header files will be found in /usr/include/fml
Forwarded: not-needed

--- a/seq_test/Makefile.am
+++ b/seq_test/Makefile.am
@@ -4,14 +4,11 @@ AUTOMAKE_OPTIONS = subdir-objects
 
 seq_test_CPPFLAGS = \
      -I../src \
-     -I../htslib \
+     -I/usr/include/fml \
      -I.. \
-     -I../fermi-lite --coverage -D_GLIBCXX_USE_CXX11_ABI=0
+     --coverage -D_GLIBCXX_USE_CXX11_ABI=0
 
 seq_test_LDADD = \
-	../fermi-lite/libfml.a \
-	../bwa/libbwa.a \
-	../htslib/libhts.a \
 	-lboost_unit_test_framework -lboost_system -lboost_timer -lboost_chrono -lbz2 -llzma
 
 seq_test_LDFLAGS = --coverage -pthread
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,6 +1,6 @@
 noinst_LIBRARIES = libseqlib.a
 
-libseqlib_a_CPPFLAGS =  -I../htslib -Wno-sign-compare
+libseqlib_a_CPPFLAGS =  -I/usr/include/fml -Wno-sign-compare
 
 libseqlib_a_SOURCES =   FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp ssw_cpp.cpp ssw.c \
 			GenomicRegion.cpp RefGenome.cpp BamWriter.cpp BamReader.cpp \
--- a/SeqLib/FermiAssembler.h
+++ b/SeqLib/FermiAssembler.h
@@ -9,9 +9,9 @@
 
 extern "C" 
 {
-#include "fermi-lite/htab.h"
-#include "fermi-lite/fml.h"
-#include "fermi-lite/bfc.h"
+#include <fml/htab.h>
+#include <fml.h>
+#include <fml/bfc.h>
 }
 namespace SeqLib {
 
--- a/src/FermiAssembler.cpp
+++ b/src/FermiAssembler.cpp
@@ -1,5 +1,5 @@
 #include "SeqLib/FermiAssembler.h"
-#include "fermi-lite/fml.h"
+#include <fml.h>
 #define MAG_MIN_NSR_COEF .1
 
 namespace SeqLib {