X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fmain.c;h=75125f872d0117d287186a72251b0e2eaeb5853f;hp=7ffc2a05f4557a1aa12a156a86dc2e15cf51ead3;hb=e42445c748ed193f8d0a4277a844fa848f30c132;hpb=fa217aa47313e2535cbd2d4bb034cfd405162662

diff --git a/bcftools/main.c b/bcftools/main.c
index 7ffc2a0..75125f8 100644
--- a/bcftools/main.c
+++ b/bcftools/main.c
@@ -5,6 +5,7 @@
 
 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
 
@@ -50,12 +51,14 @@ int main(int argc, char *argv[])
 		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, "         ld        compute all-pair r^2\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 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;