fixed compilation error

diff --git a/Makefile b/Makefile
index 8a7418e3bcfd961c31810fee6faf86713a6433d6..6a04c1b51b195c16170c3dec210719f13b8a7889 100644 (file)
--- 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 2f96d324d7c471f903cea8a7b93fb6e93be5b522..d69c771da80ef14ed925e549548f988a766ae680 100644 (file)
--- 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 89f4fa130886e388c18f5989b2c2b5bd33138526..896108ac8a1f26bf4c67bb7694fd4f71da4658cd 100644 (file)
--- 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 ec3fa746a61dcd5cf959898df9b9ec00c59712a1..7fdf41f6b26583bca9641c36ecaadfef468703fe 100644 (file)
--- 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//`; \