From 5329dbb6df3eee6a46d875b9d50e7f1a869f6b25 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Thu, 7 Jul 2011 04:37:01 +0000
Subject: [PATCH] for WIN32 compatibility

---
 Makefile.mingw      | 17 +++++++++--------
 bcftools/bcfutils.c |  5 +++++
 bcftools/call1.c    |  5 +++++
 bedidx.c            |  4 ++++
 ksort.h             |  4 ++++
 5 files changed, 27 insertions(+), 8 deletions(-)

diff --git a/Makefile.mingw b/Makefile.mingw
index a3f4b9f..7a57ffc 100644
--- a/Makefile.mingw
+++ b/Makefile.mingw
@@ -4,14 +4,15 @@ CFLAGS=		-g -Wall -O2
 DFLAGS=		-D_USE_KNETFILE -D_CURSES_LIB=2
 KNETFILE_O=	knetfile.o
 LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
-			bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o \
-			$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-AOBJS=		bam_tview.o bam_plcmd.o sam_view.o	\
+			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o \
+			$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bedidx.o
+AOBJS=		bam_tview.o bam_plcmd.o sam_view.o \
 			bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o	\
-			bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o
+			bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
+			cut_target.o phase.o bam_cat.o bam2depth.o
 BCFOBJS=	bcftools/bcf.o bcftools/fet.o bcftools/bcf2qcall.o bcftools/bcfutils.o \
-			bcftools/call1.o bcftools/index.o bcftools/kfunc.o bcftools/ld.o \
-			bcftools/prob1.o bcftools/vcf.o
+			bcftools/call1.o bcftools/index.o bcftools/kfunc.o bcftools/em.o \
+			bcftools/kmin.o bcftools/prob1.o bcftools/vcf.o bcftools/mut.o
 PROG=		samtools.exe bcftools.exe
 INCLUDES=	-I. -Iwin32
 SUBDIRS=	.
@@ -35,8 +36,8 @@ libbam.a:$(LOBJS)
 samtools.exe:$(AOBJS) libbam.a $(BCFOBJS)
 		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(BCFOBJS) $(LIBPATH) -lm -L. -lbam -Lwin32 -lz -lcurses -lws2_32
 
-bcftools.exe:$(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o
-		$(CC) $(CFLAGS) -o $@ $(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o -lm -Lwin32 -lz -lws2_32
+bcftools.exe:$(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o
+		$(CC) $(CFLAGS) -o $@ $(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o -lm -Lwin32 -lz -lws2_32
 
 razip.o:razf.h
 bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index e11cfce..9608846 100644
--- a/bcftools/bcfutils.c
+++ b/bcftools/bcfutils.c
@@ -5,6 +5,11 @@
 #include "khash.h"
 KHASH_MAP_INIT_STR(str2id, int)
 
+#ifdef _WIN32
+#define srand48(x) srand(x)
+#define drand48() ((double)rand() / RAND_MAX)
+#endif
+
 // FIXME: valgrind report a memory leak in this function. Probably it does not get deallocated...
 void *bcf_build_refhash(bcf_hdr_t *h)
 {
diff --git a/bcftools/call1.c b/bcftools/call1.c
index b2d7d4a..69bd5f7 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -8,6 +8,11 @@
 #include "kstring.h"
 #include "time.h"
 
+#ifdef _WIN32
+#define srand48(x) srand(x)
+#define lrand48() rand()
+#endif
+
 #include "kseq.h"
 KSTREAM_INIT(gzFile, gzread, 16384)
 
diff --git a/bedidx.c b/bedidx.c
index 34f0f2f..ec75a10 100644
--- a/bedidx.c
+++ b/bedidx.c
@@ -4,6 +4,10 @@
 #include <stdio.h>
 #include <zlib.h>
 
+#ifdef _WIN32
+#define drand48() ((double)rand() / RAND_MAX)
+#endif
+
 #include "ksort.h"
 KSORT_INIT_GENERIC(uint64_t)
 
diff --git a/ksort.h b/ksort.h
index fa850ab..b8b62f1 100644
--- a/ksort.h
+++ b/ksort.h
@@ -60,6 +60,10 @@
 #include <stdlib.h>
 #include <string.h>
 
+#ifdef _WIN32
+#define drand48() ((double)rand() / RAND_MAX)
+#endif
+
 typedef struct {
 	void *left, *right;
 	int depth;
-- 
2.39.2