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refactor and prepare for a new command

This commit is contained in:
Heng Li 2021-07-19 00:36:17 -04:00
parent 2411887d8e
commit cf7eaef367
1 changed files with 16 additions and 2 deletions
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18
misc/mmphase.js
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@ -255,7 +255,7 @@ function process_paf(a, opt, fp_seq, buf, ecb)
} }
} }
function main(args) function mmp_utec(args)
{ {
var c, opt = { min_rlen:20000, min_blen:10000, min_iden:0.8, min_mlen:5, max_clip_len:500, max_ratio0:0.25, dbg:false }; var c, opt = { min_rlen:20000, min_blen:10000, min_iden:0.8, min_mlen:5, max_clip_len:500, max_ratio0:0.25, dbg:false };
while ((c = getopt(args, "l:b:d:m:c:r:D")) != null) { while ((c = getopt(args, "l:b:d:m:c:r:D")) != null) {
@ -268,7 +268,7 @@ function main(args)
else if (c == 'D') opt.dbg = true; else if (c == 'D') opt.dbg = true;
} }
if (args.length - getopt.ind < 2) { if (args.length - getopt.ind < 2) {
print("Usage: utec.js [options] <map-with-cs.paf> <seq.fa>"); print("Usage: mmphase.js utec [options] <map-with-cs.paf> <seq.fa>");
print("Options:"); print("Options:");
print(" -l INT min read length [" + opt.min_rlen + "]"); print(" -l INT min read length [" + opt.min_rlen + "]");
print(" -b INT min alignment length [" + opt.min_blen + "]"); print(" -b INT min alignment length [" + opt.min_blen + "]");
@ -302,5 +302,19 @@ function main(args)
buf.destroy(); buf.destroy();
} }
function main(args)
{
if (args.length == 0) {
print("Usage: mmphase.js <command> [arguments]");
print("Commands:");
print(" utec unitig-based error correction for Nanopore reads");
exit(1);
}
var cmd = args.shift();
if (cmd == 'utec') mmp_utec(args);
else throw Error("unrecognized command: " + cmd);
}
var ret = main(arguments) var ret = main(arguments)
exit(ret) exit(ret)