void ProcessNonDaemonCommands(int argc, const char **argv) {
if (strcmp(argv[1], "index") == 0) {
if (CommandPipe == NULL) {
GenomeIndex::runIndexer(argc - 2, argv + 2);
} else {
//
// The error cases in index build don't really free memory properly, so we just don't allows it in daemon mode.
//
WriteErrorMessage("The index command is not available in daemon mode. Please run 'snap index' directly.\n");
}
} else if (strcmp(argv[1], "single") == 0 || strcmp(argv[1], "paired") == 0) {
for (int i = 1; i < argc; /* i is increased below */) {
unsigned nArgsConsumed;
if (strcmp(argv[i], "single") == 0) {
SingleAlignerContext single;
single.runAlignment(argc - i, argv + i, SNAP_VERSION, &nArgsConsumed);
} else if (strcmp(argv[i], "paired") == 0) {
PairedAlignerContext paired;
paired.runAlignment(argc - i, argv + i, SNAP_VERSION, &nArgsConsumed);
} else {
fprintf(stderr, "Invalid command: %s\n\n", argv[i]);
usage();
return;
}
_ASSERT(nArgsConsumed > 0);
i += nArgsConsumed;
}
} else {
WriteErrorMessage("Invalid command: %s\n\n", argv[1]);
usage();
}
}
int main(int argc, const char **argv)
{
printf("Welcome to SNAP version %s.\n\n", SNAP_VERSION);
if (argc < 2) {
usage();
} else if (strcmp(argv[1], "index") == 0) {
GenomeIndex::runIndexer(argc - 2, argv + 2);
} else if (strcmp(argv[1], "single") == 0) {
SingleAlignerContext single;
single.runAlignment(argc - 2, argv + 2, SNAP_VERSION);
} else if (strcmp(argv[1], "paired") == 0) {
PairedAlignerContext paired;
paired.runAlignment(argc - 2, argv + 2, SNAP_VERSION);
} else {
fprintf(stderr, "Invalid command: %s\n\n", argv[1]);
usage();
}
}
