| 51 |
|
int main(int argc, char *argv[]) |
| 52 |
|
{ |
| 53 |
|
|
| 54 |
< |
GArgs args(argc, argv, "fasta;fastq;gff;all;help;mapped-only;hAMGaqo:"); |
| 54 |
> |
GArgs args(argc, argv, "fasta;fastq;gff;all;help;mapped-only;" |
| 55 |
> |
"hAMGaqo:"); |
| 56 |
|
args.printError(USAGE, true); |
| 57 |
|
if (args.getOpt('h') || args.getOpt("help") || args.startNonOpt()==0) { |
| 58 |
|
GMessage(USAGE); |
| 59 |
|
return 1; |
| 60 |
|
} |
| 61 |
+ |
args.printCmdLine(stderr); |
| 62 |
|
|
| 63 |
|
all_reads=(args.getOpt('A') || args.getOpt("all")); |
| 64 |
|
mapped_only=(args.getOpt('M') || args.getOpt("mapped-only")); |
