Imported Upstream version 0.1.15

[samtools.git] / bcftools / main.c

diff --git a/bcftools/main.c b/bcftools/main.c
index 7ffc2a05f4557a1aa12a156a86dc2e15cf51ead3..75125f872d0117d287186a72251b0e2eaeb5853f 100644 (file)
--- 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 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
 
 
 #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, "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);
                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;
        else {
                fprintf(stderr, "[main] Unrecognized command.\n");
                return 1;