Package: libseqlib / 1.1.2+dfsg-1~bpo9+1

fml_include_path.patch Patch series | download
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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

--- a/seq_test/Makefile.am
+++ b/seq_test/Makefile.am
@@ -2,14 +2,11 @@ bin_PROGRAMS = seq_test
 
 seq_test_CPPFLAGS = \
      -I../src \
-     -I../htslib \
+     -I/usr/include/fml \
      -I.. \
-     -I../fermi-lite --coverage
+     --coverage
 
 seq_test_LDADD = \
-	../fermi-lite/libfml.a \
-	../bwa/libbwa.a \
-	../htslib/libhts.a \
 	-lboost_unit_test_framework -lboost_system -lboost_timer -lboost_chrono
 
 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../ -I../htslib -Wno-sign-compare
+libseqlib_a_CPPFLAGS = -I../ -I../htslib -I/usr/include/fml -Wno-sign-compare
 
 libseqlib_a_SOURCES =   FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp jsoncpp.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 {