From 6f1c7227019c299bd9df4c4187ca29e0baad1c4b Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Wed, 4 Aug 2010 01:13:00 +0000
Subject: [PATCH] fixed compilation error

---
 Makefile          | 10 +++++-----
 bam2bcf.c         |  2 +-
 bam2bcf.h         |  2 +-
 bcftools/Makefile |  4 ++--
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/Makefile b/Makefile
index 8a7418e..6a04c1b 100644
--- a/Makefile
+++ b/Makefile
@@ -9,7 +9,7 @@ AOBJS=		bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o	\
 			bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o	\
 			bamtk.o kaln.o bam_mcns.o bam2bcf.o
 PROG=		samtools
-INCLUDES=	-Ibcftools
+INCLUDES=	-I.
 SUBDIRS=	. bcftools misc
 LIBPATH=
 LIBCURSES=	-lcurses # -lXCurses
@@ -25,7 +25,7 @@ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
 		list='$(SUBDIRS)'; for subdir in $$list; do \
 			cd $$subdir; \
 			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-				LIBPATH="$(LIBPATH)" $$target || exit 1; \
+				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
 			cd $$wdir; \
 		done;
 
@@ -53,7 +53,7 @@ bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
 sam.o:sam.h bam.h
 bam_import.o:bam.h kseq.h khash.h razf.h
 bam_pileup.o:bam.h razf.h ksort.h
-bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h bam_mcns.h bcf.h bam2bcf.h
+bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h bam_mcns.h bcftools/bcf.h bam2bcf.h
 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
 bam_lpileup.o:bam.h ksort.h
 bam_tview.o:bam.h faidx.h bam_maqcns.h
@@ -62,8 +62,8 @@ bam_sort.o:bam.h ksort.h razf.h
 bam_md.o:bam.h faidx.h
 glf.o:glf.h
 sam_header.o:sam_header.h khash.h
-bcf.o:bcf.h
-bam2bcf.o:bam2bcf.h bcf.h
+bcf.o:bcftools/bcf.h
+bam2bcf.o:bam2bcf.h bcftools/bcf.h
 
 faidx.o:faidx.h razf.h khash.h
 faidx_main.o:faidx.h razf.h
diff --git a/bam2bcf.c b/bam2bcf.c
index 2f96d32..d69c771 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 #include "kstring.h"
 #include "bam2bcf.h"
-#include "bcf.h"
+#include "bcftools/bcf.h"
 
 extern	void ks_introsort_uint32_t(size_t n, uint32_t a[]);
 
diff --git a/bam2bcf.h b/bam2bcf.h
index 89f4fa1..896108a 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,7 +2,7 @@
 #define BAM2BCF_H
 
 #include <stdint.h>
-#include "bcf.h"
+#include "bcftools/bcf.h"
 
 struct __bcf_callaux_t;
 typedef struct __bcf_callaux_t bcf_callaux_t;
diff --git a/bcftools/Makefile b/bcftools/Makefile
index ec3fa74..7fdf41f 100644
--- a/bcftools/Makefile
+++ b/bcftools/Makefile
@@ -5,13 +5,13 @@ LOBJS=		bcf.o bcfutils.o prob1.o index.o
 OMISC=		..
 AOBJS=		vcfout.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o
 PROG=		bcftools
-INCLUDES=	-I..
+INCLUDES=	
 SUBDIRS=	.
 
 .SUFFIXES:.c .o
 
 .c.o:
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@
 
 all-recur lib-recur clean-recur cleanlocal-recur install-recur:
 		@target=`echo $@ | sed s/-recur//`; \
-- 
2.39.2