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don't add a new command

This commit is contained in:
Heng Li 2021-07-19 10:57:48 -04:00
parent cf7eaef367
commit f3af29a8aa
1 changed files with 29 additions and 35 deletions
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64
misc/mmphase.js
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@ -96,8 +96,9 @@ function parse_events(t, ev, id, buf)
var x = st; var x = st;
while ((m = re.exec(cs)) != null) { while ((m = re.exec(cs)) != null) {
var l; var l;
if (m[2] != null) { if (m[2] != null) { // an identitcal match ":\d+"
l = parseInt(m[2]); l = parseInt(m[2]);
// [start, end, type, index, changed_base]
ev.push([x, x + l, 0, id]); ev.push([x, x + l, 0, id]);
} else { } else {
if (m[4] == '*') { if (m[4] == '*') {
@ -143,6 +144,7 @@ function find_het_sub(ev, a, opt)
sh += h[i][j][1] - h[i][j][0]; sh += h[i][j][1] - h[i][j][0];
for (var j = 0; j < d[i].length; ++j) for (var j = 0; j < d[i].length; ++j)
dh += d[i][j][1]; dh += d[i][j][1];
// // [start, end, index, ?, ?, ?, ?, identity, mlen]
b[i] = [a[i][2], a[i][3], i, h[i].length, sh, d[i].length, dh, a[i][9] / a[i][10], a[i][9]]; b[i] = [a[i][2], a[i][3], i, h[i].length, sh, d[i].length, dh, a[i][9] / a[i][10], a[i][9]];
} }
return b; return b;
@ -222,17 +224,19 @@ function ec_core(b, n_a, ev, buf, ecb)
function process_paf(a, opt, fp_seq, buf, ecb) function process_paf(a, opt, fp_seq, buf, ecb)
{ {
if (a.length == 0) return; if (a.length == 0) return;
var len = a[0][1]; var len = a[0][1], name = a[0][0], seq = null;
if (len < opt.min_rlen) return; if (len < opt.min_rlen) return;
var ret; if (fp_seq) {
while ((ret = read_fastx(fp_seq, buf, name, seq)) != null) var ret;
if (ret[0] == a[0][0]) while ((ret = read_fastx(fp_seq, buf)) != null)
break; if (ret[0] == a[0][0])
if (ret == null) break;
throw Error("failed to find sequence for read '" + a[0][0] + "'"); if (ret == null)
var name = ret[0], seq = ret[1], len = a[0][1]; throw Error("failed to find sequence for read '" + a[0][0] + "'");
if (seq.length != len) name = ret[0], seq = ret[1];
throw Error("inconsistent length for read '" + name + "'"); if (seq.length != len)
throw Error("inconsistent length for read '" + name + "'");
}
filter_paf(a, opt); filter_paf(a, opt);
if (a.length == 0) return; if (a.length == 0) return;
var ev = []; var ev = [];
@ -244,18 +248,22 @@ function process_paf(a, opt, fp_seq, buf, ecb)
var b = find_het_sub(ev, a, opt); var b = find_het_sub(ev, a, opt);
flt_utg(b, opt); flt_utg(b, opt);
if (b.length == 0) return; if (b.length == 0) return;
buf.set(seq, 0);
ec_core(b, a.length, ev, buf, ecb);
if (opt.dbg) { if (opt.dbg) {
for (var i = 0; i < b.length; ++i) for (var i = 0; i < b.length; ++i)
print(b[i].join("\t"), a[b[i][2]][5]); print(b[i].join("\t"), a[b[i][2]][5]);
} else { }
print(">" + name); if (seq == null) {
print(ecb); } else { // error correction
buf.set(seq, 0);
ec_core(b, a.length, ev, buf, ecb);
if (!opt.dbg) {
print(">" + name);
print(ecb);
}
} }
} }
function mmp_utec(args) function main(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) {
@ -267,8 +275,8 @@ function mmp_utec(args)
else if (c == 'r') opt.max_ratio0 = parseFloat(getopt.arg); else if (c == 'r') opt.max_ratio0 = parseFloat(getopt.arg);
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 < 1) {
print("Usage: mmphase.js utec [options] <map-with-cs.paf> <seq.fa>"); print("Usage: mmphase.js [options] <map-with-cs.paf> [reads.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 + "]");
@ -280,7 +288,7 @@ function mmp_utec(args)
} }
var buf = new Bytes(), ecb = new Bytes(); var buf = new Bytes(), ecb = new Bytes();
var fp_paf = new File(args[getopt.ind]); var fp_paf = new File(args[getopt.ind]);
var fp_seq = new File(args[getopt.ind+1]); var fp_seq = args.length - getopt.ind >= 2? new File(args[getopt.ind+1]) : null;
var a = []; var a = [];
while (fp_paf.readline(buf) >= 0) { while (fp_paf.readline(buf) >= 0) {
var t = buf.toString().split("\t"); var t = buf.toString().split("\t");
@ -296,25 +304,11 @@ function mmp_utec(args)
} }
if (a.length >= 0) if (a.length >= 0)
process_paf(a, opt, fp_seq, buf, ecb); process_paf(a, opt, fp_seq, buf, ecb);
fp_seq.close(); if (fp_seq) fp_seq.close();
fp_paf.close(); fp_paf.close();
ecb.destroy(); ecb.destroy();
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)