added calls and description for bam_calnh.

diff --git a/bamtk.c b/bamtk.c
index 8ba25811d2771e171fa08899015449618838f265..52b12df86edb655f21e9d73d1325a0c505f20eb7 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -19,6 +19,7 @@ int bam_rmdup(int argc, char *argv[]);
 int bam_flagstat(int argc, char *argv[]);
 int bam_fillmd(int argc, char *argv[]);
 int bam_idxstats(int argc, char *argv[]);
+int bam_calnh(int argc, char **argv);
 int main_samview(int argc, char *argv[]);
 int main_import(int argc, char *argv[]);
 int main_reheader(int argc, char *argv[]);
@@ -55,6 +56,7 @@ static int usage()
        fprintf(stderr, "         cat         concatenate BAMs\n");
        fprintf(stderr, "         targetcut   cut fosmid regions (for fosmid pool only)\n");
        fprintf(stderr, "         phase       phase heterozygotes\n");
+       fprintf(stderr, "         calnh       calculate NH tags\n");
        fprintf(stderr, "\n");
 #ifdef _WIN32
        fprintf(stderr, "\
@@ -98,6 +100,7 @@ int main(int argc, char *argv[])
                fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
                return 1;
        }
+       else if (strcmp(argv[1], "calnh") == 0) return bam_calnh(argc-1, argv+1);
 #if _CURSES_LIB != 0
        else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif