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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
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 {
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