INNER CODE UNIT · JavaScript
mg_cmd_anno
lh3/minigraph · misc/mgutils.js:174
function mg_cmd_anno(args)
{
var c, min_rm_div = 0.2, min_rm_sc = 300, micro_cap = 6, min_feat_len = 30, min_centro_len = 200, mobile = false, max_mobile_div = 2.0, min_segdup_frac = 0.2, min_ld_frac = 0.7;
var fn_rmout = null, fn_etrf = null, fn_dust = null, fn_gap = null, fn_paf = null, fn_centro = null, fn_bb = null, fn_sd = null, fn_ld = null;
while ((c = getopt(args, "e:p:g:d:r:c:l:S:L:b:s:mx:X:")) != null) {
if (c == 'l') min_feat_len = parseInt(getopt.arg);
else if (c == 'S') min_segdup_frac = parseFloat(getopt.arg);
else if (c == 'm') mobile = true;
else if (c == 'e') fn_etrf = getopt.arg;
else if (c == 'p') fn_paf = getopt.arg;
else if (c == 'g') fn_gap = getopt.arg;
else if (c == 'd') fn_dust = getopt.arg;
else if (c == 'r') fn_rmout = getopt.arg;
else if (c == 'c') fn_centro = getopt.arg;
else if (c == 'b') fn_bb = getopt.arg;
else if (c == 's') fn_sd = getopt.arg;
else if (c == 'x') fn_ld = getopt.arg;
}