INNER CODE UNIT · C
pair
lh3/ksw2 · cli.c:163
int c, i, pair = 1, w = -1, flag = 0, rep = 1, zdrop = -1, no_kalloc = 0;
char *algo = "extd", *s;
int8_t mat[25];
ksw_extz_t ez;
gzFile fp[2];
while ((c = getopt(argc, argv, "t:w:R:rsgz:A:B:O:E:Ka")) >= 0) {
if (c == 't') algo = optarg;
else if (c == 'w') w = atoi(optarg);
else if (c == 'R') rep = atoi(optarg);
else if (c == 'z') zdrop = atoi(optarg);
else if (c == 'r') flag |= KSW_EZ_RIGHT;
else if (c == 's') flag |= KSW_EZ_SCORE_ONLY;
else if (c == 'g') flag |= KSW_EZ_APPROX_MAX | KSW_EZ_APPROX_DROP;
else if (c == 'K') no_kalloc = 1;
else if (c == 'A') a = atoi(optarg);
else if (c == 'B') b = atoi(optarg);
else if (c == 'a') pair = 0;