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 faidx_main(int argc, char *argv[]);
int glf3_view_main(int argc, char *argv[]);
fprintf(stderr, " merge merge sorted alignments\n");
fprintf(stderr, " rmdup remove PCR duplicates\n");
fprintf(stderr, " reheader replace BAM header\n");
+ 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, "\n");
else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "reheader") == 0) return main_reheader(argc-1, argv+1);
+ else if (strcmp(argv[1], "cat") == 0) return main_cat(argc-1, argv+1);
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);
#if _CURSES_LIB != 0