Description: Adapt examples for Debian package
 The location of the fast5 hdf header file is slightly different and
 the HDF library/header locations are different.
Author: Afif Elghraoui <afif@debian.org>
Forwarded: not-needed
Last-Update: 2016-10-20
--- fast5.orig/src/Makefile
+++ fast5/src/Makefile
@@ -4,9 +4,9 @@
 .DELETE_ON_ERROR:
 .PHONY: all help list clean check_hdf5
 
-HDF5_DIR = /usr/local
-HDF5_INCLUDE_DIR = ${HDF5_DIR}/include
-HDF5_LIB_DIR = ${HDF5_DIR}/lib
+HDF5_DIR = /usr
+HDF5_INCLUDE_DIR ?= ${HDF5_DIR}/include/hdf5/serial
+HDF5_LIB_DIR ?= $(wildcard ${HDF5_DIR}/lib/*/hdf5/serial)
 HDF5_LIB = hdf5
 
 TARGETS = f5dump f5dump-full hdf5-mod f5-mod
@@ -29,5 +29,5 @@
 	@[ -f "${HDF5_INCLUDE_DIR}/H5pubconf.h" ] || { echo "HDF5 headers not found" >&2; exit 1; }
 	@[ -f "${HDF5_LIB_DIR}/lib${HDF5_LIB}.so" ] || [ -f "${HDF5_LIB_DIR}/lib${HDF5_LIB}.a" ] || { echo "HDF5 library not found" >&2; exit 1; }
 
-%: %.cpp fast5.hpp hdf5_tools.hpp | check_hdf5
-	${CXX} -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic -isystem ${HDF5_INCLUDE_DIR} -o $@ $< -L${HDF5_LIB_DIR} -Wl,--rpath=${HDF5_LIB_DIR} -l${HDF5_LIB} -lpthread -lz -ldl
+%: %.cpp | check_hdf5
+	${CXX} ${CPPFLAGS} ${CXXFLAGS} -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic -isystem ${HDF5_INCLUDE_DIR} -o $@ $< -L${HDF5_LIB_DIR} -Wl,--rpath=${HDF5_LIB_DIR} -l${HDF5_LIB} -lpthread -lz -ldl
--- fast5.orig/src/hdf5-mod.cpp
+++ fast5/src/hdf5-mod.cpp
@@ -2,7 +2,7 @@
 #include <iostream>
 #include <string>
 
-#include "hdf5_tools.hpp"
+#include <fast5/hdf5_tools.hpp>
 
 using namespace std;
 using namespace hdf5;
--- fast5.orig/src/f5dump.cpp
+++ fast5/src/f5dump.cpp
@@ -2,7 +2,7 @@
 #include <iostream>
 #include <string>
 
-#include "fast5.hpp"
+#include <fast5.hpp>
 
 using namespace std;
 
--- fast5.orig/src/f5dump-full.cpp
+++ fast5/src/f5dump-full.cpp
@@ -2,7 +2,7 @@
 #include <iostream>
 #include <string>
 
-#include "fast5.hpp"
+#include <fast5.hpp>
 
 using namespace std;