merged a few converters to paftools
This commit is contained in:
Heng Li
parent
66c5e71fa8
commit
3465b04724
198
misc/paf2aln.js
198
misc/paf2aln.js
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@ -1,198 +0,0 @@
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#!/usr/bin/env k8
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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, line_len = 80, fmt = "aln";
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while ((c = getopt(arguments, "f:l:")) != null) {
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if (c == 'f') {
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fmt = getopt.arg;
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if (fmt != "aln" && fmt != "lastz-cigar" && fmt != "maf")
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throw Error("format must be one of aln, lastz-cigar and maf");
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} else if (c == 'l') line_len = parseInt(getopt.arg);
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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] <in.paf>");
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print("Options:");
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print(" -f STR output format: aln (BLAST-like), maf or lastz-cigar [aln]");
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print(" -l INT line length in BLAST-like output [80]");
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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 == '=' || 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(); // these are used to show padded alignment
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var re_cs = /([:=\-\+\*])(\d+|[A-Za-z]+)/g;
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var re_cg = /(\d+)([MIDNSH])/g;
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var buf = new Bytes();
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var file = arguments[getopt.ind] == "-"? new File() : new File(arguments[getopt.ind]);
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var lineno = 0;
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if (fmt == "maf") 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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++lineno;
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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 (fmt == "lastz-cigar") { // LASTZ-cigar output
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var cg = (m = /\tcg:Z:(\S+)/.exec(line)) != null? m[1] : null;
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if (cg == null) {
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warn("WARNING: converting to LASTZ-cigar format requires the 'cg' tag, which is absent on line " + lineno);
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continue;
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}
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var score = (m = /\tAS:i:(\d+)/.exec(line)) != null? m[1] : 0;
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var out = ['cigar:', t[0], t[2], t[3], t[4], t[5], t[7], t[8], '+', score];
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while ((m = re_cg.exec(cg)) != null)
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out.push(m[2], m[1]);
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print(out.join(" "));
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} else if (fmt == "maf") { // MAF output
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var cs = (m = /\tcs:Z:(\S+)/.exec(line)) != null? m[1] : null;
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if (cs == null) {
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warn("WARNING: converting to MAF requires the 'cs' tag, which is absent on line " + lineno);
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continue;
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}
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while ((m = re_cs.exec(cs)) != null) {
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if (m[1] == ':')
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throw Error("converting to MAF only works with 'minimap2 --cs=long'");
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update_aln(s_ref, s_qry, s_mid, m[1], m[2], elen);
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}
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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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} else { // BLAST-like output
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var cs = (m = /\tcs:Z:(\S+)/.exec(line)) != null? m[1] : null;
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if (cs == null) {
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warn("WARNING: converting to BLAST-like alignment requires the 'cs' tag, which is absent on line " + lineno);
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continue;
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}
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line = line.replace(/\tc[sg]:Z:\S+/g, ""); // get rid of cs or cg tags
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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_cs.exec(cs)) != null) {
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if (m[1] == ':') m[2] = Array(parseInt(m[2]) + 1).join("=");
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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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367
misc/paftools.js
367
misc/paftools.js
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@ -329,6 +329,363 @@ function paf_call(args)
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file.close();
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}
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/**************************
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*** Conversion related ***
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**************************/
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function paf_view(args)
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{
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var c, line_len = 80, fmt = "aln";
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while ((c = getopt(args, "f:l:")) != null) {
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if (c == 'f') {
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fmt = getopt.arg;
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if (fmt != "aln" && fmt != "lastz-cigar" && fmt != "maf")
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throw Error("format must be one of aln, lastz-cigar and maf");
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} else if (c == 'l') line_len = parseInt(getopt.arg);
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}
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if (line_len == 0) line_len = 0x7fffffff;
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if (getopt.ind == args.length) {
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print("Usage: paftools.js view [options] <in.paf>");
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print("Options:");
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print(" -f STR output format: aln (BLAST-like), maf or lastz-cigar [aln]");
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print(" -l INT line length in BLAST-like output [80]");
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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 == '=' || 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(); // these are used to show padded alignment
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var re_cs = /([:=\-\+\*])(\d+|[A-Za-z]+)/g;
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var re_cg = /(\d+)([MIDNSH])/g;
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var buf = new Bytes();
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var file = args[getopt.ind] == "-"? new File() : new File(args[getopt.ind]);
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var lineno = 0;
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if (fmt == "maf") 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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++lineno;
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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 (fmt == "lastz-cigar") { // LASTZ-cigar output
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var cg = (m = /\tcg:Z:(\S+)/.exec(line)) != null? m[1] : null;
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if (cg == null) {
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warn("WARNING: converting to LASTZ-cigar format requires the 'cg' tag, which is absent on line " + lineno);
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continue;
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}
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var score = (m = /\tAS:i:(\d+)/.exec(line)) != null? m[1] : 0;
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var out = ['cigar:', t[0], t[2], t[3], t[4], t[5], t[7], t[8], '+', score];
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while ((m = re_cg.exec(cg)) != null)
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out.push(m[2], m[1]);
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print(out.join(" "));
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} else if (fmt == "maf") { // MAF output
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var cs = (m = /\tcs:Z:(\S+)/.exec(line)) != null? m[1] : null;
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if (cs == null) {
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warn("WARNING: converting to MAF requires the 'cs' tag, which is absent on line " + lineno);
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continue;
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}
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while ((m = re_cs.exec(cs)) != null) {
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if (m[1] == ':')
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throw Error("converting to MAF only works with 'minimap2 --cs=long'");
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update_aln(s_ref, s_qry, s_mid, m[1], m[2], elen);
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}
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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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} else { // BLAST-like output
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var cs = (m = /\tcs:Z:(\S+)/.exec(line)) != null? m[1] : null;
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if (cs == null) {
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warn("WARNING: converting to BLAST-like alignment requires the 'cs' tag, which is absent on line " + lineno);
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continue;
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}
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line = line.replace(/\tc[sg]:Z:\S+/g, ""); // get rid of cs or cg tags
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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_cs.exec(cs)) != null) {
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if (m[1] == ':') m[2] = Array(parseInt(m[2]) + 1).join("=");
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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);
|
||||
++n_blocks;
|
||||
}
|
||||
print("//");
|
||||
}
|
||||
}
|
||||
file.close();
|
||||
buf.destroy();
|
||||
|
||||
s_ref.destroy(); s_qry.destroy(); s_mid.destroy();
|
||||
}
|
||||
|
||||
function paf_sam2paf(args)
|
||||
{
|
||||
var c, pri_only = false;
|
||||
while ((c = getopt(args, "p")) != null)
|
||||
if (c == 'p') pri_only = true;
|
||||
|
||||
var file = args.length == getopt.ind || args[getopt.ind] == "-"? new File() : new File(args[getopt.ind]);
|
||||
var buf = new Bytes();
|
||||
var re = /(\d+)([MIDSHNX=])/g;
|
||||
|
||||
var len = {}, lineno = 0;
|
||||
while (file.readline(buf) >= 0) {
|
||||
var m, n_cigar = 0, line = buf.toString();
|
||||
++lineno;
|
||||
if (line.charAt(0) == '@') {
|
||||
if (/^@SQ/.test(line)) {
|
||||
var name = (m = /\tSN:(\S+)/.exec(line)) != null? m[1] : null;
|
||||
var l = (m = /\tLN:(\d+)/.exec(line)) != null? parseInt(m[1]) : null;
|
||||
if (name != null && l != null) len[name] = l;
|
||||
}
|
||||
continue;
|
||||
}
|
||||
var t = line.split("\t");
|
||||
var flag = parseInt(t[1]);
|
||||
if (t[9] != '*' && t[10] != '*' && t[9].length != t[10].length) throw Error("ERROR at line " + lineno + ": inconsistent SEQ and QUAL lengths - " + t[9].length + " != " + t[10].length);
|
||||
if (t[2] == '*' || (flag&4)) continue;
|
||||
if (pri_only && (flag&0x100)) continue;
|
||||
var tlen = len[t[2]];
|
||||
if (tlen == null) throw Error("ERROR at line " + lineno + ": can't find the length of contig " + t[2]);
|
||||
var nn = (m = /\tnn:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 0;
|
||||
var NM = (m = /\tNM:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : null;
|
||||
var have_NM = NM == null? false : true;
|
||||
NM += nn;
|
||||
var clip = [0, 0], I = [0, 0], D = [0, 0], M = 0, N = 0, ql = 0, tl = 0, mm = 0, ext_cigar = false;
|
||||
while ((m = re.exec(t[5])) != null) {
|
||||
var l = parseInt(m[1]);
|
||||
if (m[2] == 'M') M += l, ql += l, tl += l, ext_cigar = false;
|
||||
else if (m[2] == 'I') ++I[0], I[1] += l, ql += l;
|
||||
else if (m[2] == 'D') ++D[0], D[1] += l, tl += l;
|
||||
else if (m[2] == 'N') N += l, tl += l;
|
||||
else if (m[2] == 'S') clip[M == 0? 0 : 1] = l, ql += l;
|
||||
else if (m[2] == 'H') clip[M == 0? 0 : 1] = l;
|
||||
else if (m[2] == '=') M += l, ql += l, tl += l, ext_cigar = true;
|
||||
else if (m[2] == 'X') M += l, ql += l, tl += l, mm += l, ext_cigar = true;
|
||||
++n_cigar;
|
||||
}
|
||||
if (n_cigar > 65535)
|
||||
warn("WARNING at line " + lineno + ": " + n_cigar + " CIGAR operations");
|
||||
if (tl + parseInt(t[3]) - 1 > tlen) {
|
||||
warn("WARNING at line " + lineno + ": alignment end position larger than ref length; skipped");
|
||||
continue;
|
||||
}
|
||||
if (t[9] != '*' && t[9].length != ql) {
|
||||
warn("WARNING at line " + lineno + ": SEQ length inconsistent with CIGAR (" + t[9].length + " != " + ql + "); skipped");
|
||||
continue;
|
||||
}
|
||||
if (!have_NM || ext_cigar) NM = I[1] + D[1] + mm;
|
||||
if (NM < I[1] + D[1] + mm) {
|
||||
warn("WARNING at line " + lineno + ": NM is less than the total number of gaps (" + NM + " < " + (I[1]+D[1]+mm) + ")");
|
||||
NM = I[1] + D[1] + mm;
|
||||
}
|
||||
var extra = ["mm:i:"+(NM-I[1]-D[1]), "io:i:"+I[0], "in:i:"+I[1], "do:i:"+D[0], "dn:i:"+D[1]];
|
||||
var match = M - (NM - I[1] - D[1]);
|
||||
var blen = M + I[1] + D[1];
|
||||
var qlen = M + I[1] + clip[0] + clip[1];
|
||||
var qs, qe;
|
||||
if (flag&16) qs = clip[1], qe = qlen - clip[0];
|
||||
else qs = clip[0], qe = qlen - clip[1];
|
||||
var ts = parseInt(t[3]) - 1, te = ts + M + D[1] + N;
|
||||
var qname = t[0];
|
||||
if ((flag&1) && (flag&0x40)) qname += '/1';
|
||||
if ((flag&1) && (flag&0x80)) qname += '/2';
|
||||
var a = [qname, qlen, qs, qe, flag&16? '-' : '+', t[2], tlen, ts, te, match, blen, t[4]];
|
||||
print(a.join("\t"), extra.join("\t"));
|
||||
}
|
||||
|
||||
buf.destroy();
|
||||
file.close();
|
||||
}
|
||||
|
||||
function paf_splice2bed(args)
|
||||
{
|
||||
var colors = ["0,128,255", "255,0,0", "0,192,0"];
|
||||
|
||||
function print_lines(a, fmt)
|
||||
{
|
||||
if (a.length == 0) return;
|
||||
if (fmt == "bed") {
|
||||
var n_pri = 0;
|
||||
for (var i = 0; i < a.length; ++i)
|
||||
if (a[i][8] == 0) ++n_pri;
|
||||
if (n_pri > 1) {
|
||||
for (var i = 0; i < a.length; ++i)
|
||||
if (a[i][8] == 0) a[i][8] = 1;
|
||||
} else if (n_pri == 0) {
|
||||
warn("Warning: " + a[0][3] + " doesn't have a primary alignment");
|
||||
}
|
||||
for (var i = 0; i < a.length; ++i) {
|
||||
a[i][8] = colors[a[i][8]];
|
||||
print(a[i].join("\t"));
|
||||
}
|
||||
}
|
||||
a.length = 0;
|
||||
}
|
||||
|
||||
var re = /(\d+)([MIDNSH])/g;
|
||||
var c, fmt = "bed", fn_name_conv = null;
|
||||
while ((c = getopt(args, "f:n:")) != null) {
|
||||
if (c == 'f') fmt = getopt.arg;
|
||||
else if (c == 'n') fn_name_conv = getopt.arg;
|
||||
}
|
||||
if (getopt.ind == args.length) {
|
||||
warn("Usage: paftools.js splice2bed <in.paf>|<in.sam>");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
var conv = null;
|
||||
if (fn_name_conv != null) {
|
||||
conv = new Map();
|
||||
var file = new File(fn_name_conv);
|
||||
var buf = new Bytes();
|
||||
while (file.readline(buf) >= 0) {
|
||||
var t = buf.toString().split("\t");
|
||||
conv.put(t[0], t[1]);
|
||||
}
|
||||
buf.destroy();
|
||||
file.close();
|
||||
}
|
||||
|
||||
var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
|
||||
var buf = new Bytes();
|
||||
var a = [];
|
||||
while (file.readline(buf) >= 0) {
|
||||
var line = buf.toString();
|
||||
if (line.charAt(0) == '@') continue; // skip SAM header lines
|
||||
var t = line.split("\t");
|
||||
var is_pri = false, cigar = null, a1;
|
||||
var qname = conv != null? conv.get(t[0]) : null;
|
||||
if (qname != null) t[0] = qname;
|
||||
if (t.length >= 10 && t[4] != '+' && t[4] != '-' && /^\d+/.test(t[1])) { // SAM
|
||||
var flag = parseInt(t[1]);
|
||||
if (flag&1) t[0] += '/' + (flag>>6&3);
|
||||
}
|
||||
if (a.length && a[0][3] != t[0]) {
|
||||
print_lines(a, fmt);
|
||||
a = [];
|
||||
}
|
||||
if (t.length >= 12 && (t[4] == '+' || t[4] == '-')) { // PAF
|
||||
for (var i = 12; i < t.length; ++i) {
|
||||
if (t[i].substr(0, 5) == 'cg:Z:') {
|
||||
cigar = t[i].substr(5);
|
||||
} else if (t[i].substr(0, 5) == 's2:i:') {
|
||||
is_pri = true;
|
||||
}
|
||||
}
|
||||
a1 = [t[5], t[7], t[8], t[0], Math.floor(t[9]/t[10]*1000), t[4]];
|
||||
} else if (t.length >= 10) { // SAM
|
||||
var flag = parseInt(t[1]);
|
||||
if ((flag&4) || a[2] == '*') continue;
|
||||
cigar = t[5];
|
||||
is_pri = (flag&0x100)? false : true;
|
||||
a1 = [t[2], parseInt(t[3])-1, null, t[0], 1000, (flag&16)? '-' : '+'];
|
||||
} else {
|
||||
throw Error("unrecognized input format");
|
||||
}
|
||||
if (cigar == null) throw Error("missing CIGAR");
|
||||
var m, x0 = 0, x = 0, bs = [], bl = [];
|
||||
while ((m = re.exec(cigar)) != null) {
|
||||
if (m[2] == 'M' || m[2] == 'D') {
|
||||
x += parseInt(m[1]);
|
||||
} else if (m[2] == 'N') {
|
||||
bs.push(x0);
|
||||
bl.push(x - x0);
|
||||
x += parseInt(m[1]);
|
||||
x0 = x;
|
||||
}
|
||||
}
|
||||
bs.push(x0);
|
||||
bl.push(x - x0);
|
||||
// write the BED12 line
|
||||
if (a1[2] == null) a1[2] = a1[1] + x;
|
||||
a1.push(a1[1], a1[2]); // thick start/end is the same as start/end
|
||||
a1.push(is_pri? 0 : 2, bs.length, bl.join(",")+",", bs.join(",")+",");
|
||||
a.push(a1);
|
||||
}
|
||||
print_lines(a, fmt);
|
||||
buf.destroy();
|
||||
file.close();
|
||||
if (conv != null) conv.destroy();
|
||||
}
|
||||
|
||||
/**************************
|
||||
*** Evaluation related ***
|
||||
**************************/
|
||||
|
|
@ -640,6 +997,7 @@ function paf_pbsim2fq(args)
|
|||
buf2.destroy();
|
||||
}
|
||||
|
||||
// evaluate overlap sensitivity
|
||||
function paf_ov_eval(args)
|
||||
{
|
||||
var c, min_ovlp = 2000, min_frac = 0.95, min_mapq = 10;
|
||||
|
|
@ -720,6 +1078,10 @@ function main(args)
|
|||
if (args.length == 0) {
|
||||
print("Usage: paftools.js <command> [arguments]");
|
||||
print("Commands:");
|
||||
print(" view convert PAF to BLAST-like (for eyeballing) or MAF");
|
||||
print(" sam2paf convert SAM to PAF");
|
||||
print(" splice2bed convert spliced alignment in PAF/SAM to BED12");
|
||||
print("");
|
||||
print(" call call variants from asm-to-ref alignment with the cs tag");
|
||||
print("");
|
||||
print(" mapeval evaluate mapping accuracy using mason2/PBSIM-simulated FASTQ");
|
||||
|
|
@ -730,7 +1092,10 @@ function main(args)
|
|||
}
|
||||
|
||||
var cmd = args.shift();
|
||||
if (cmd == 'call') paf_call(args);
|
||||
if (cmd == 'view') paf_view(args);
|
||||
else if (cmd == 'sam2paf') paf_sam2paf(args);
|
||||
else if (cmd == 'splice2bed') paf_splice2bed(args);
|
||||
else if (cmd == 'call') paf_call(args);
|
||||
else if (cmd == 'mapeval') paf_mapeval(args);
|
||||
else if (cmd == 'mason2fq') paf_mason2fq(args);
|
||||
else if (cmd == 'pbsim2fq') paf_pbsim2fq(args);
|
||||
|
|
|
|||
116
misc/sam2paf.js
116
misc/sam2paf.js
|
|
@ -1,116 +0,0 @@
|
|||
#!/usr/bin/env k8
|
||||
|
||||
var getopt = function(args, ostr) {
|
||||
var oli; // option letter list index
|
||||
if (typeof(getopt.place) == 'undefined')
|
||||
getopt.ind = 0, getopt.arg = null, getopt.place = -1;
|
||||
if (getopt.place == -1) { // update scanning pointer
|
||||
if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
|
||||
getopt.place = -1;
|
||||
return null;
|
||||
}
|
||||
if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
|
||||
++getopt.ind;
|
||||
getopt.place = -1;
|
||||
return null;
|
||||
}
|
||||
}
|
||||
var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
|
||||
if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
|
||||
if (optopt == '-') return null; // if the user didn't specify '-' as an option, assume it means null.
|
||||
if (getopt.place < 0) ++getopt.ind;
|
||||
return '?';
|
||||
}
|
||||
if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
|
||||
getopt.arg = null;
|
||||
if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
|
||||
} else { // need an argument
|
||||
if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
|
||||
getopt.arg = args[getopt.ind].substr(getopt.place);
|
||||
else if (args.length <= ++getopt.ind) { // no arg
|
||||
getopt.place = -1;
|
||||
if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
|
||||
return '?';
|
||||
} else getopt.arg = args[getopt.ind]; // white space
|
||||
getopt.place = -1;
|
||||
++getopt.ind;
|
||||
}
|
||||
return optopt;
|
||||
}
|
||||
|
||||
var c, pri_only = false;
|
||||
while ((c = getopt(arguments, "p")) != null)
|
||||
if (c == 'p') pri_only = true;
|
||||
|
||||
var file = arguments.length == getopt.ind || arguments[getopt.ind] == "-"? new File() : new File(arguments[getopt.ind]);
|
||||
var buf = new Bytes();
|
||||
var re = /(\d+)([MIDSHNX=])/g;
|
||||
|
||||
var len = {}, lineno = 0;
|
||||
while (file.readline(buf) >= 0) {
|
||||
var m, n_cigar = 0, line = buf.toString();
|
||||
++lineno;
|
||||
if (line.charAt(0) == '@') {
|
||||
if (/^@SQ/.test(line)) {
|
||||
var name = (m = /\tSN:(\S+)/.exec(line)) != null? m[1] : null;
|
||||
var l = (m = /\tLN:(\d+)/.exec(line)) != null? parseInt(m[1]) : null;
|
||||
if (name != null && l != null) len[name] = l;
|
||||
}
|
||||
continue;
|
||||
}
|
||||
var t = line.split("\t");
|
||||
var flag = parseInt(t[1]);
|
||||
if (t[9] != '*' && t[10] != '*' && t[9].length != t[10].length) throw Error("ERROR at line " + lineno + ": inconsistent SEQ and QUAL lengths - " + t[9].length + " != " + t[10].length);
|
||||
if (t[2] == '*' || (flag&4)) continue;
|
||||
if (pri_only && (flag&0x100)) continue;
|
||||
var tlen = len[t[2]];
|
||||
if (tlen == null) throw Error("ERROR at line " + lineno + ": can't find the length of contig " + t[2]);
|
||||
var nn = (m = /\tnn:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 0;
|
||||
var NM = (m = /\tNM:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : null;
|
||||
var have_NM = NM == null? false : true;
|
||||
NM += nn;
|
||||
var clip = [0, 0], I = [0, 0], D = [0, 0], M = 0, N = 0, ql = 0, tl = 0, mm = 0, ext_cigar = false;
|
||||
while ((m = re.exec(t[5])) != null) {
|
||||
var l = parseInt(m[1]);
|
||||
if (m[2] == 'M') M += l, ql += l, tl += l, ext_cigar = false;
|
||||
else if (m[2] == 'I') ++I[0], I[1] += l, ql += l;
|
||||
else if (m[2] == 'D') ++D[0], D[1] += l, tl += l;
|
||||
else if (m[2] == 'N') N += l, tl += l;
|
||||
else if (m[2] == 'S') clip[M == 0? 0 : 1] = l, ql += l;
|
||||
else if (m[2] == 'H') clip[M == 0? 0 : 1] = l;
|
||||
else if (m[2] == '=') M += l, ql += l, tl += l, ext_cigar = true;
|
||||
else if (m[2] == 'X') M += l, ql += l, tl += l, mm += l, ext_cigar = true;
|
||||
++n_cigar;
|
||||
}
|
||||
if (n_cigar > 65535)
|
||||
warn("WARNING at line " + lineno + ": " + n_cigar + " CIGAR operations");
|
||||
if (tl + parseInt(t[3]) - 1 > tlen) {
|
||||
warn("WARNING at line " + lineno + ": alignment end position larger than ref length; skipped");
|
||||
continue;
|
||||
}
|
||||
if (t[9] != '*' && t[9].length != ql) {
|
||||
warn("WARNING at line " + lineno + ": SEQ length inconsistent with CIGAR (" + t[9].length + " != " + ql + "); skipped");
|
||||
continue;
|
||||
}
|
||||
if (!have_NM || ext_cigar) NM = I[1] + D[1] + mm;
|
||||
if (NM < I[1] + D[1] + mm) {
|
||||
warn("WARNING at line " + lineno + ": NM is less than the total number of gaps (" + NM + " < " + (I[1]+D[1]+mm) + ")");
|
||||
NM = I[1] + D[1] + mm;
|
||||
}
|
||||
var extra = ["mm:i:"+(NM-I[1]-D[1]), "io:i:"+I[0], "in:i:"+I[1], "do:i:"+D[0], "dn:i:"+D[1]];
|
||||
var match = M - (NM - I[1] - D[1]);
|
||||
var blen = M + I[1] + D[1];
|
||||
var qlen = M + I[1] + clip[0] + clip[1];
|
||||
var qs, qe;
|
||||
if (flag&16) qs = clip[1], qe = qlen - clip[0];
|
||||
else qs = clip[0], qe = qlen - clip[1];
|
||||
var ts = parseInt(t[3]) - 1, te = ts + M + D[1] + N;
|
||||
var qname = t[0];
|
||||
if ((flag&1) && (flag&0x40)) qname += '/1';
|
||||
if ((flag&1) && (flag&0x80)) qname += '/2';
|
||||
var a = [qname, qlen, qs, qe, flag&16? '-' : '+', t[2], tlen, ts, te, match, blen, t[4]];
|
||||
print(a.join("\t"), extra.join("\t"));
|
||||
}
|
||||
|
||||
buf.destroy();
|
||||
file.close();
|
||||
|
|
@ -1,150 +0,0 @@
|
|||
#!/usr/bin/env k8
|
||||
|
||||
var getopt = function(args, ostr) {
|
||||
var oli; // option letter list index
|
||||
if (typeof(getopt.place) == 'undefined')
|
||||
getopt.ind = 0, getopt.arg = null, getopt.place = -1;
|
||||
if (getopt.place == -1) { // update scanning pointer
|
||||
if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
|
||||
getopt.place = -1;
|
||||
return null;
|
||||
}
|
||||
if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
|
||||
++getopt.ind;
|
||||
getopt.place = -1;
|
||||
return null;
|
||||
}
|
||||
}
|
||||
var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
|
||||
if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
|
||||
if (optopt == '-') return null; // if the user didn't specify '-' as an option, assume it means null.
|
||||
if (getopt.place < 0) ++getopt.ind;
|
||||
return '?';
|
||||
}
|
||||
if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
|
||||
getopt.arg = null;
|
||||
if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
|
||||
} else { // need an argument
|
||||
if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
|
||||
getopt.arg = args[getopt.ind].substr(getopt.place);
|
||||
else if (args.length <= ++getopt.ind) { // no arg
|
||||
getopt.place = -1;
|
||||
if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
|
||||
return '?';
|
||||
} else getopt.arg = args[getopt.ind]; // white space
|
||||
getopt.place = -1;
|
||||
++getopt.ind;
|
||||
}
|
||||
return optopt;
|
||||
}
|
||||
|
||||
var colors = ["0,128,255", "255,0,0", "0,192,0"];
|
||||
|
||||
function print_lines(a, fmt) {
|
||||
if (a.length == 0) return;
|
||||
if (fmt == "bed") {
|
||||
var n_pri = 0;
|
||||
for (var i = 0; i < a.length; ++i)
|
||||
if (a[i][8] == 0) ++n_pri;
|
||||
if (n_pri > 1) {
|
||||
for (var i = 0; i < a.length; ++i)
|
||||
if (a[i][8] == 0) a[i][8] = 1;
|
||||
} else if (n_pri == 0) {
|
||||
warn("Warning: " + a[0][3] + " doesn't have a primary alignment");
|
||||
}
|
||||
for (var i = 0; i < a.length; ++i) {
|
||||
a[i][8] = colors[a[i][8]];
|
||||
print(a[i].join("\t"));
|
||||
}
|
||||
}
|
||||
a.length = 0;
|
||||
}
|
||||
|
||||
function main(args) {
|
||||
var re = /(\d+)([MIDNSH])/g;
|
||||
var c, fmt = "bed", fn_name_conv = null;
|
||||
while ((c = getopt(args, "f:n:")) != null) {
|
||||
if (c == 'f') fmt = getopt.arg;
|
||||
else if (c == 'n') fn_name_conv = getopt.arg;
|
||||
}
|
||||
if (getopt.ind == args.length) {
|
||||
warn("Usage: k8 splice2bed.js <in.paf>|<in.sam>");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
var conv = null;
|
||||
if (fn_name_conv != null) {
|
||||
conv = new Map();
|
||||
var file = new File(fn_name_conv);
|
||||
var buf = new Bytes();
|
||||
while (file.readline(buf) >= 0) {
|
||||
var t = buf.toString().split("\t");
|
||||
conv.put(t[0], t[1]);
|
||||
}
|
||||
buf.destroy();
|
||||
file.close();
|
||||
}
|
||||
|
||||
var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
|
||||
var buf = new Bytes();
|
||||
var a = [];
|
||||
while (file.readline(buf) >= 0) {
|
||||
var line = buf.toString();
|
||||
if (line.charAt(0) == '@') continue; // skip SAM header lines
|
||||
var t = line.split("\t");
|
||||
var is_pri = false, cigar = null, a1;
|
||||
var qname = conv != null? conv.get(t[0]) : null;
|
||||
if (qname != null) t[0] = qname;
|
||||
if (t.length >= 10 && t[4] != '+' && t[4] != '-' && /^\d+/.test(t[1])) { // SAM
|
||||
var flag = parseInt(t[1]);
|
||||
if (flag&1) t[0] += '/' + (flag>>6&3);
|
||||
}
|
||||
if (a.length && a[0][3] != t[0]) {
|
||||
print_lines(a, fmt);
|
||||
a = [];
|
||||
}
|
||||
if (t.length >= 12 && (t[4] == '+' || t[4] == '-')) { // PAF
|
||||
for (var i = 12; i < t.length; ++i) {
|
||||
if (t[i].substr(0, 5) == 'cg:Z:') {
|
||||
cigar = t[i].substr(5);
|
||||
} else if (t[i].substr(0, 5) == 's2:i:') {
|
||||
is_pri = true;
|
||||
}
|
||||
}
|
||||
a1 = [t[5], t[7], t[8], t[0], Math.floor(t[9]/t[10]*1000), t[4]];
|
||||
} else if (t.length >= 10) { // SAM
|
||||
var flag = parseInt(t[1]);
|
||||
if ((flag&4) || a[2] == '*') continue;
|
||||
cigar = t[5];
|
||||
is_pri = (flag&0x100)? false : true;
|
||||
a1 = [t[2], parseInt(t[3])-1, null, t[0], 1000, (flag&16)? '-' : '+'];
|
||||
} else {
|
||||
throw Error("unrecognized input format");
|
||||
}
|
||||
if (cigar == null) throw Error("missing CIGAR");
|
||||
var m, x0 = 0, x = 0, bs = [], bl = [];
|
||||
while ((m = re.exec(cigar)) != null) {
|
||||
if (m[2] == 'M' || m[2] == 'D') {
|
||||
x += parseInt(m[1]);
|
||||
} else if (m[2] == 'N') {
|
||||
bs.push(x0);
|
||||
bl.push(x - x0);
|
||||
x += parseInt(m[1]);
|
||||
x0 = x;
|
||||
}
|
||||
}
|
||||
bs.push(x0);
|
||||
bl.push(x - x0);
|
||||
// write the BED12 line
|
||||
if (a1[2] == null) a1[2] = a1[1] + x;
|
||||
a1.push(a1[1], a1[2]); // thick start/end is the same as start/end
|
||||
a1.push(is_pri? 0 : 2, bs.length, bl.join(",")+",", bs.join(",")+",");
|
||||
a.push(a1);
|
||||
}
|
||||
print_lines(a, fmt);
|
||||
buf.destroy();
|
||||
file.close();
|
||||
if (conv != null) conv.destroy();
|
||||
}
|
||||
|
||||
main(arguments);
|
||||
Loading…
Reference in New Issue