Imported Upstream version 0.1.9

[samtools.git] / bcftools / main.c

diff --git a/bcftools/main.c b/bcftools/main.c
new file mode 100644 (file)
index 0000000..7ffc2a0
--- /dev/null
+++ b/bcftools/main.c
@@ -0,0 +1,64 @@
+#include <string.h>
+#include <stdlib.h>
+#include <sys/stat.h>
+#include "bcf.h"
+
+int bcfview(int argc, char *argv[]);
+int bcf_main_index(int argc, char *argv[]);
+
+#define BUF_SIZE 0x10000
+
+int bcf_cat(int n, char * const *fn)
+{
+       int i;
+       bcf_t *out;
+       uint8_t *buf;
+       buf = malloc(BUF_SIZE);
+       out = bcf_open("-", "w");
+       for (i = 0; i < n; ++i) {
+               bcf_t *in;
+               bcf_hdr_t *h;
+               off_t end;
+               struct stat s;
+               in = bcf_open(fn[i], "r");
+               h = bcf_hdr_read(in);
+               if (i == 0) bcf_hdr_write(out, h);
+               bcf_hdr_destroy(h);
+#ifdef _USE_KNETFILE
+               fstat(knet_fileno(in->fp->x.fpr), &s);
+               end = s.st_size - 28;
+               while (knet_tell(in->fp->x.fpr) < end) {
+                       int size = knet_tell(in->fp->x.fpr) + BUF_SIZE < end? BUF_SIZE : end - knet_tell(in->fp->x.fpr);
+                       knet_read(in->fp->x.fpr, buf, size);
+                       fwrite(buf, 1, size, out->fp->x.fpw);
+               }
+#else
+               abort(); // FIXME: not implemented
+#endif
+               bcf_close(in);
+       }
+       bcf_close(out);
+       free(buf);
+       return 0;
+}
+
+int main(int argc, char *argv[])
+{
+       if (argc == 1) {
+               fprintf(stderr, "\n");
+               fprintf(stderr, "Usage:   bcftools <command> <arguments>\n\n");
+               fprintf(stderr, "Command: view      print, extract, convert and call SNPs from BCF\n");
+               fprintf(stderr, "         index     index BCF\n");
+               fprintf(stderr, "         cat       concatenate BCFs\n");
+               fprintf(stderr, "\n");
+               return 1;
+       }
+       if (strcmp(argv[1], "view") == 0) return bcfview(argc-1, argv+1);
+       else if (strcmp(argv[1], "index") == 0) return bcf_main_index(argc-1, argv+1);
+       else if (strcmp(argv[1], "cat") == 0) return bcf_cat(argc-2, argv+2);
+       else {
+               fprintf(stderr, "[main] Unrecognized command.\n");
+               return 1;
+       }
+       return 0;
+}