int main(int argc, char *argv[])
{
if (argc < 2) return usage();
if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
else if (strcmp(argv[1], "view") == 0 || strcmp(argv[1], "mview") == 0 ) return main_view(argc-1, argv+1);
else if (strcmp(argv[1], "fmf") == 0 ) return main_fmf(argc-1, argv+1);
else if (strcmp(argv[1], "getalt") == 0) return main_getalt(argc-1, argv+1);
else if (strcmp(argv[1], "bcfidx") == 0) return main_bcfidx(argc-1, argv+1);
else if (strcmp(argv[1], "version") == 0) {
puts(BGT_VERSION);
return 0;
} else {
fprintf(stderr, "[E::%s] unrecognized command '%s'\n", __func__, argv[1]);
return 1;
}
}
int samtools_main(int argc, char *argv[])
{
#ifdef _WIN32
setmode(fileno(stdout), O_BINARY);
setmode(fileno(stdin), O_BINARY);
#endif
if (argc < 2) { usage(pysamerr); return 1; }
if (strcmp(argv[1], "help") == 0 || strcmp(argv[1], "--help") == 0) {
if (argc == 2) { usage(stdout); return 0; }
// Otherwise change "samtools help COMMAND [...]" to "samtools COMMAND";
// main_xyz() functions by convention display the subcommand's usage
// when invoked without any arguments.
argv++;
argc = 2;
}
int ret = 0;
if (strcmp(argv[1], "view") == 0) ret = main_samview(argc-1, argv+1);
else if (strcmp(argv[1], "import") == 0) ret = main_import(argc-1, argv+1);
else if (strcmp(argv[1], "mpileup") == 0) ret = bam_mpileup(argc-1, argv+1);
else if (strcmp(argv[1], "merge") == 0) ret = bam_merge(argc-1, argv+1);
else if (strcmp(argv[1], "sort") == 0) ret = bam_sort(argc-1, argv+1);
else if (strcmp(argv[1], "index") == 0) ret = bam_index(argc-1, argv+1);
else if (strcmp(argv[1], "idxstats") == 0) ret = bam_idxstats(argc-1, argv+1);
else if (strcmp(argv[1], "faidx") == 0) ret = faidx_main(argc-1, argv+1);
else if (strcmp(argv[1], "dict") == 0) ret = dict_main(argc-1, argv+1);
else if (strcmp(argv[1], "fixmate") == 0) ret = bam_mating(argc-1, argv+1);
else if (strcmp(argv[1], "rmdup") == 0) ret = bam_rmdup(argc-1, argv+1);
else if (strcmp(argv[1], "flagstat") == 0) ret = bam_flagstat(argc-1, argv+1);
else if (strcmp(argv[1], "calmd") == 0) ret = bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "fillmd") == 0) ret = bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "reheader") == 0) ret = main_reheader(argc-1, argv+1);
else if (strcmp(argv[1], "cat") == 0) ret = main_cat(argc-1, argv+1);
else if (strcmp(argv[1], "targetcut") == 0) ret = main_cut_target(argc-1, argv+1);
else if (strcmp(argv[1], "phase") == 0) ret = main_phase(argc-1, argv+1);
else if (strcmp(argv[1], "depth") == 0) ret = main_depth(argc-1, argv+1);
else if (strcmp(argv[1], "bam2fq") == 0 ||
strcmp(argv[1], "fastq") == 0 ||
strcmp(argv[1], "fasta") == 0) ret = main_bam2fq(argc-1, argv+1);
else if (strcmp(argv[1], "pad2unpad") == 0) ret = main_pad2unpad(argc-1, argv+1);
else if (strcmp(argv[1], "depad") == 0) ret = main_pad2unpad(argc-1, argv+1);
else if (strcmp(argv[1], "bedcov") == 0) ret = main_bedcov(argc-1, argv+1);
else if (strcmp(argv[1], "bamshuf") == 0) ret = main_bamshuf(argc-1, argv+1);
else if (strcmp(argv[1], "collate") == 0) ret = main_bamshuf(argc-1, argv+1);
else if (strcmp(argv[1], "stats") == 0) ret = main_stats(argc-1, argv+1);
else if (strcmp(argv[1], "flags") == 0) ret = main_flags(argc-1, argv+1);
else if (strcmp(argv[1], "split") == 0) ret = main_split(argc-1, argv+1);
else if (strcmp(argv[1], "quickcheck") == 0) ret = main_quickcheck(argc-1, argv+1);
else if (strcmp(argv[1], "addreplacerg") == 0) ret = main_addreplacerg(argc-1, argv+1);
else if (strcmp(argv[1], "pileup") == 0) {
fprintf(pysamerr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
return 1;
}
else if (strcmp(argv[1], "tview") == 0) ret = bam_tview_main(argc-1, argv+1);
else if (strcmp(argv[1], "--version") == 0) {
printf(
"samtools %s\n"
"Using htslib %s\n"
"Copyright (C) 2015 Genome Research Ltd.\n",
samtools_version(), hts_version());
}
else if (strcmp(argv[1], "--version-only") == 0) {
printf("%s+htslib-%s\n", samtools_version(), hts_version());
}
else {
fprintf(pysamerr, "[main] unrecognized command '%s'\n", argv[1]);
return 1;
}
return ret;
}