-
- if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
- else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
- else if (strcmp(argv[1], "mpileup") == 0) return bam_mpileup(argc-1, argv+1);
- else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
- else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
- else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
- else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
- else if (strcmp(argv[1], "idxstats") == 0) return bam_idxstats(argc-1, argv+1);
- else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
- else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
- else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
- 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);
- 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);
+ int retval = 0;
+
+ if (strcmp(argv[1], "view") == 0) retval = main_samview(argc-1, argv+1);
+ else if (strcmp(argv[1], "import") == 0) retval = main_import(argc-1, argv+1);
+ else if (strcmp(argv[1], "mpileup") == 0) retval = bam_mpileup(argc-1, argv+1);
+ else if (strcmp(argv[1], "merge") == 0) retval = bam_merge(argc-1, argv+1);
+ else if (strcmp(argv[1], "sort") == 0) retval = bam_sort(argc-1, argv+1);
+ else if (strcmp(argv[1], "index") == 0) retval = bam_index(argc-1, argv+1);
+ else if (strcmp(argv[1], "faidx") == 0) retval = faidx_main(argc-1, argv+1);
+ else if (strcmp(argv[1], "idxstats") == 0) retval = bam_idxstats(argc-1, argv+1);
+ else if (strcmp(argv[1], "fixmate") == 0) retval = bam_mating(argc-1, argv+1);
+ else if (strcmp(argv[1], "rmdup") == 0) retval = bam_rmdup(argc-1, argv+1);
+ else if (strcmp(argv[1], "flagstat") == 0) retval = bam_flagstat(argc-1, argv+1);
+ else if (strcmp(argv[1], "calmd") == 0) retval = bam_fillmd(argc-1, argv+1);
+ else if (strcmp(argv[1], "fillmd") == 0) retval = bam_fillmd(argc-1, argv+1);
+ else if (strcmp(argv[1], "reheader") == 0) retval = main_reheader(argc-1, argv+1);
+ else if (strcmp(argv[1], "cat") == 0) retval = main_cat(argc-1, argv+1);
+ else if (strcmp(argv[1], "targetcut") == 0) retval = main_cut_target(argc-1, argv+1);
+ else if (strcmp(argv[1], "phase") == 0) retval = main_phase(argc-1, argv+1);
+ else if (strcmp(argv[1], "depth") == 0)
+ {
+ retval = main_depth(argc-1, argv+1);
+ }
+
+ else if (strcmp(argv[1], "bam2fq") == 0) retval = main_bam2fq(argc-1, argv+1);