- if (argc < 3) {
- fprintf(stderr, "Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
- return 1;
- }
- in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
- out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
- bam_mating_core(in, out);
+ int c, remove_reads=0;
+ while ((c = getopt(argc, argv, "r")) >= 0) {
+ switch (c) {
+ case 'r': remove_reads=1; break;
+ }
+ }
+ if (optind+1 >= argc) usage();
+ in = (strcmp(argv[optind], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[optind], "r");
+ out = (strcmp(argv[optind+1], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[optind+1], "w");
+ bam_mating_core(in, out, remove_reads);