int main_phase(int argc, char *argv[]);
int main_cat(int argc, char *argv[]);
int main_depth(int argc, char *argv[]);
+int main_bam2fq(int argc, char *argv[]);
int faidx_main(int argc, char *argv[]);
else if (strcmp(argv[1], "targetcut") == 0) return main_cut_target(argc-1, argv+1);
else if (strcmp(argv[1], "phase") == 0) return main_phase(argc-1, argv+1);
else if (strcmp(argv[1], "depth") == 0) return main_depth(argc-1, argv+1);
+ else if (strcmp(argv[1], "bam2fq") == 0) return main_bam2fq(argc-1, argv+1);
+ else if (strcmp(argv[1], "pileup") == 0) {
+ fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
+ return 1;
+ }
#if _CURSES_LIB != 0
else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
#endif