for WIN32 compatibility

diff --git a/Makefile.mingw b/Makefile.mingw
index a3f4b9fe6b33f7ec6d706279fdac89ee50f87810..7a57ffc0c7457c5fcfb65dd8585bd3ee3cb1114c 100644 (file)
--- 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 e11cfce2663029d480d03c8bebf7b338a9b3b973..9608846bef3b435edf470d3b3ae8a075431e82b3 100644 (file)
--- 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 b2d7d4a197b112ea10c6caf3ad4a9a13d95b1298..69bd5f7700698dfe39207695328220a4d8eba248 100644 (file)
--- 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 34f0f2fb3ba0e40aaab31e4c8eca4140e4a5d458..ec75a1067f5905c69ead868ff42d2073189bb690 100644 (file)
--- 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 fa850ab0762a9225bae5b3bcad6739a3bb6a3c27..b8b62f189c557a8aa77fbdfbb93e7dafb3acba14 100644 (file)
--- 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;