Subject: upstream copies libsam headers
Description: use Debian libraries instead of embedded headers
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 2013-08-05
Forwarded: no
--- a/sparsePregraph/Makefile
+++ b/sparsePregraph/Makefile
@@ -10,7 +10,7 @@
 			build_preArc.o pregraph_sparse.o io_func.o\
 			global.o convert_soapdenovo.o
 PROG=           
-INCLUDES=	-I./inc
+INCLUDES=	-I./inc -I/usr/include/samtools
 SUBDIRS=    . 
 LIBPATH=	-L./inc -L/usr/lib64
 LIBS=       -pthread -lz
--- a/sparsePregraph/inc/stdinc.h
+++ b/sparsePregraph/inc/stdinc.h
@@ -40,4 +40,4 @@
 
 
 
-
+#include <stdbool.h>
--- a/standardPregraph/Makefile
+++ b/standardPregraph/Makefile
@@ -25,7 +25,7 @@
 		readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o \
 		cutTip_graph2.o linearEdge.o kmerhash.o read2edge.o iterate.o
 PROG=       SOAPdenovo-63mer
-INCLUDES=   -Iinc
+INCLUDES=   -Iinc -I/usr/include/samtools
 SUBDIRS=    .
 LIBPATH=    -L./inc -L/lib64 -L/usr/lib64
 LIBS=       -pthread -lz -lm 
--- a/standardPregraph/inc/stdinc.h
+++ b/standardPregraph/inc/stdinc.h
@@ -32,3 +32,4 @@
 #include "types.h"
 #include <aio.h>
 #include <errno.h>
+#include <stdbool.h>
