#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, "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);
- if (strcmp(argv[1], "index") == 0) return bcf_main_index(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;