-extern int main_samview(int argc, char *argv[]);
-extern int main_import(int argc, char *argv[]);
-extern int bam_pileup(int argc, char *argv[]);
-extern int bam_merge(int argc, char *argv[]);
-extern int bam_sort(int argc, char *argv[]);
-extern int bam_index(int argc, char *argv[]);
-extern int faidx_main(int argc, char *argv[]);
-extern int bam_mating(int argc, char *argv[]);
-extern int bam_rmdup(int argc, char *argv[]);
-extern int glf3_view_main(int argc, char *argv[]);
-extern int bam_flagstat(int argc, char *argv[]);
-extern int bam_fillmd(int argc, char *argv[]);
+int bam_taf2baf(int argc, char *argv[]);
+int bam_mpileup(int argc, char *argv[]);
+int bam_merge(int argc, char *argv[]);
+int bam_index(int argc, char *argv[]);
+int bam_sort(int argc, char *argv[]);
+int bam_tview_main(int argc, char *argv[]);
+int bam_mating(int argc, char *argv[]);
+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 main_samview(int argc, char *argv[]);
+int main_import(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
+int main_cut_target(int argc, char *argv[]);
+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[]);