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[]);
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, "\
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