X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fmain.c;h=26377e18e1ae93a9dce32822e61cf73cedb8755a;hb=674ffee7adcfc928f5039777180206fdebc5539b;hp=e271efd6b3afb6b7f63b9d317da4a849959e4072;hpb=86329087668959dbb63af0e0ca97597c23c9678e;p=samtools.git

diff --git a/bcftools/main.c b/bcftools/main.c
index e271efd..26377e1 100644
--- a/bcftools/main.c
+++ b/bcftools/main.c
@@ -1,9 +1,47 @@
 #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[]);
+int bcf_main_pwld(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[])
 {
@@ -12,11 +50,14 @@ int main(int argc, char *argv[])
 		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], "ld") == 0) return bcf_main_pwld(argc-1, argv+1);
+	else if (strcmp(argv[1], "cat") == 0) return bcf_cat(argc-2, argv+2); // cat is different ...
 	else {
 		fprintf(stderr, "[main] Unrecognized command.\n");
 		return 1;