INNER CODE UNIT · JavaScript
mg_cmd_getlcr
lh3/minigraph · misc/mgutils-es6.js:232
function mg_cmd_getlcr(args) {
let ext = 5, min_lcr = 0.7, min_ac = 5, ref_idx = 0;
for (const o of getopt(args, "a:r:e:f:")) {
if (o.opt == "-r") ref_idx = parseInt(o.arg);
else if (o.opt == "-e") ext = parseInt(o.arg);
else if (o.opt == "-f") min_lcr = parseFloat(o.arg);
else if (o.opt == "-a") min_ac = parseInt(o.arg);
}
if (args.length == 0) {
print("Usage: mgutils-es6.js getlcr [options] <merged.bed>");
print("Options:");
print(` -r INT index of the reference sample [${ref_idx}]`);
print(` -f FLOAT min fraction LCR [${min_lcr}]`);
print(` -a INT min allele count [${min_ac}]`);
print(` -e INT extend by INT-bp on each side in output [${ext}]`);
return 1;
}
const re = /([^\s=;]+)=([^\s=;]+)/g;