INNER CODE UNIT · JavaScript
mg_cmd_joinfa
lh3/minigraph · misc/mgutils.js:136
function mg_cmd_joinfa(args)
{
var c, len_n = 20, min_len = 150, name = "decoy-cat";
while ((c = getopt(args, "n:l:s:")) != null) {
if (c == 'l') min_len = parseInt(getopt.arg);
else if (c == 'n') len_n = parseInt(getopt.arg);
else if (c == 's') name = getopt.arg;
}
if (args.length - getopt.ind < 1) {
print("Usage: mgutils.js joinfa [options] <in.fa>");
return;
}
var seq = new Bytes(), seq1 = new Bytes(), lineno = 0, nn = new Bytes();
for (var i = 0; i < len_n; ++i) nn.set(78);
var buf = new Bytes();
var file = new File(args[getopt.ind]);
while (file.readline(buf) >= 0) {
++lineno;