mirror of
https://github.com/lh3/minimap2.git
synced 2026-09-25 05:58:13 +08:00
Merge branch 'cs-tag' into dev
This commit is contained in:
Heng Li
+171
@@ -0,0 +1,171 @@
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var getopt = function(args, ostr) {
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var oli; // option letter list index
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if (typeof(getopt.place) == 'undefined')
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getopt.ind = 0, getopt.arg = null, getopt.place = -1;
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if (getopt.place == -1) { // update scanning pointer
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if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
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getopt.place = -1;
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return null;
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}
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if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
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++getopt.ind;
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getopt.place = -1;
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return null;
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}
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}
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var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
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if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
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if (optopt == '-') return null; // if the user didn't specify '-' as an option, assume it means null.
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if (getopt.place < 0) ++getopt.ind;
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return '?';
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}
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if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
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getopt.arg = null;
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if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
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} else { // need an argument
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if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
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getopt.arg = args[getopt.ind].substr(getopt.place);
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else if (args.length <= ++getopt.ind) { // no arg
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getopt.place = -1;
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if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
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return '?';
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} else getopt.arg = args[getopt.ind]; // white space
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getopt.place = -1;
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++getopt.ind;
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}
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return optopt;
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}
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var c, maf_out = false, line_len = 80;
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while ((c = getopt(arguments, "ml:")) != null) {
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if (c == 'm') maf_out = true;
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else if (c == 'l') line_len = parseInt(getopt.arg); // TODO: not implemented yet
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}
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if (line_len == 0) line_len = 0x7fffffff;
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if (getopt.ind == arguments.length) {
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print("Usage: k8 paf2aln.js [options] <with-cs.paf>");
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print("Options:");
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print(" -m MAF output (BLAST-like output by default)");
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print(" -l INT line length in BLAST-like output [80]");
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print("");
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print("Note: this script only works when minimap2 is run with option '-S'");
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exit(1);
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}
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function padding_str(x, len, right)
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{
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var s = x.toString();
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if (s.length < len) {
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if (right) s += Array(len - s.length + 1).join(" ");
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else s = Array(len - s.length + 1).join(" ") + s;
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}
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return s;
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}
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function update_aln(s_ref, s_qry, s_mid, type, seq, slen)
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{
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var l = type == '*'? 1 : seq.length;
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if (type == '=') {
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s_ref.set(seq);
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s_qry.set(seq);
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s_mid.set(Array(l+1).join("|"));
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slen[0] += l, slen[1] += l;
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} else if (type == '*') {
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s_ref.set(seq.charAt(0));
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s_qry.set(seq.charAt(1));
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s_mid.set(' ');
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slen[0] += 1, slen[1] += 1;
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} else if (type == '+') {
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s_ref.set(Array(l+1).join("-"));
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s_qry.set(seq);
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s_mid.set(Array(l+1).join(" "));
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slen[1] += l;
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} else if (type == '-') {
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s_ref.set(seq);
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s_qry.set(Array(l+1).join("-"));
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s_mid.set(Array(l+1).join(" "));
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slen[0] += l;
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}
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}
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function print_aln(rs, qs, strand, slen, elen, s_ref, s_qry, s_mid)
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{
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print(["Ref+:", padding_str(rs + slen[0] + 1, 10, false), s_ref.toString(), padding_str(rs + elen[0], 10, true)].join(" "));
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print(" " + s_mid.toString());
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var st, en;
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if (strand == '+') st = qs + slen[1] + 1, en = qs + elen[1];
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else st = qs - slen[1], en = qs - elen[1] + 1;
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print(["Qry" + strand + ":", padding_str(st, 10, false), s_qry.toString(), padding_str(en , 10, true)].join(" "));
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}
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var s_ref = new Bytes(), s_qry = new Bytes(), s_mid = new Bytes();
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var re = /([=\-\+\*])([A-Za-z]+)/g;
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var buf = new Bytes();
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var file = new File(arguments[getopt.ind]);
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if (maf_out) print("##maf version=1\n");
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while (file.readline(buf) >= 0) {
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var m, line = buf.toString();
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var t = line.split("\t", 12);
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if ((m = /\tcs:Z:(\S+)/.exec(line)) == null) continue;
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var cs = m[1];
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s_ref.length = s_qry.length = s_mid.length = 0;
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var slen = [0, 0], elen = [0, 0];
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if (maf_out) {
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while ((m = re.exec(cs)) != null)
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update_aln(s_ref, s_qry, s_mid, m[1], m[2], elen);
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if (maf_out) {
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var score = (m = /\tAS:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 0;
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var len = t[0].length > t[5].length? t[0].length : t[5].length;
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print("a " + score);
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print(["s", padding_str(t[5], len, true), padding_str(t[7], 10, false), padding_str(parseInt(t[8]) - parseInt(t[7]), 10, false),
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"+", padding_str(t[6], 10, false), s_ref.toString()].join(" "));
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var qs, qe, ql = parseInt(t[1]);
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if (t[4] == '+') {
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qs = parseInt(t[2]);
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qe = parseInt(t[3]);
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} else {
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qs = ql - parseInt(t[3]);
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qe = ql - parseInt(t[2]);
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}
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print(["s", padding_str(t[0], len, true), padding_str(qs, 10, false), padding_str(qe - qs, 10, false),
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t[4], padding_str(ql, 10, false), s_qry.toString()].join(" "));
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print("");
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}
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} else {
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line = line.replace(/\tc[sg]:Z:\S+/g, "");
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print('>' + line);
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var rs = parseInt(t[7]), qs = t[4] == '+'? parseInt(t[2]) : parseInt(t[3]);
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var n_blocks = 0;
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while ((m = re.exec(cs)) != null) {
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var start = 0, rest = m[1] == '*'? 1 : m[2].length;
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while (rest > 0) {
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var l_proc;
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if (s_ref.length + rest >= line_len) {
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l_proc = line_len - s_ref.length;
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update_aln(s_ref, s_qry, s_mid, m[1], m[1] == '*'? m[2] : m[2].substr(start, l_proc), elen);
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if (n_blocks > 0) print("");
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print_aln(rs, qs, t[4], slen, elen, s_ref, s_qry, s_mid);
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++n_blocks;
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s_ref.length = s_qry.length = s_mid.length = 0;
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slen[0] = elen[0], slen[1] = elen[1];
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} else {
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l_proc = rest;
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update_aln(s_ref, s_qry, s_mid, m[1], m[1] == '*'? m[2] : m[2].substr(start, l_proc), elen);
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}
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rest -= l_proc, start += l_proc;
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}
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}
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if (s_ref.length > 0) {
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if (n_blocks > 0) print("");
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print_aln(rs, qs, t[4], slen, elen, s_ref, s_qry, s_mid);
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++n_blocks;
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}
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print("//");
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}
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}
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file.close();
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buf.destroy();
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s_ref.destroy(); s_qry.destroy(); s_mid.destroy();
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