diff --git a/misc/mmphase.js b/misc/mmphase.js index 8fec7d3..92bb680 100755 --- a/misc/mmphase.js +++ b/misc/mmphase.js @@ -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 }; 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; } if (args.length - getopt.ind < 2) { - print("Usage: utec.js [options] "); + print("Usage: mmphase.js utec [options] "); print("Options:"); print(" -l INT min read length [" + opt.min_rlen + "]"); print(" -b INT min alignment length [" + opt.min_blen + "]"); @@ -302,5 +302,19 @@ function main(args) buf.destroy(); } +function main(args) +{ + if (args.length == 0) { + print("Usage: mmphase.js [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) exit(ret)