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renamed simulation-related scripts
This commit is contained in:
Heng Li
@@ -0,0 +1,152 @@
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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, max_mapq = 60, mode = 0, err_out_q = 256, print_err = false, ovlp_ratio = 0.1, cap_short_mapq = false;
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while ((c = getopt(arguments, "Q:r:m:c")) != null) {
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if (c == 'Q') err_out_q = parseInt(getopt.arg), print_err = true;
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else if (c == 'r') ovlp_ratio = parseFloat(getopt.arg);
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else if (c == 'm') mode = parseInt(getopt.arg);
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else if (c == 'c') cap_short_mapq = true;
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}
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var file = arguments.length == getopt.ind? new File() : new File(arguments[getopt.ind]);
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var buf = new Bytes();
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var tot = [], err = [];
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for (var q = 0; q <= max_mapq; ++q)
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tot[q] = err[q] = 0;
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function is_correct(s, b)
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{
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if (s[0] != b[0] || s[3] != b[3]) return false;
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var o, l;
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if (s[1] < b[1]) {
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if (s[2] <= b[1]) return false;
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o = (s[2] < b[2]? s[2] : b[2]) - b[1];
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l = (s[2] > b[2]? s[2] : b[2]) - s[1];
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} else {
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if (b[2] <= s[1]) return false;
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o = (s[2] < b[2]? s[2] : b[2]) - s[1];
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l = (s[2] > b[2]? s[2] : b[2]) - b[1];
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}
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return o/l > ovlp_ratio? true : false;
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}
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function count_err(qname, a, tot, err, mode)
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{
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var s = qname.split("!");
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if (a.length == 0) return;
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if (s.length < 5 || (s[4] != '+' && s[4] != '-'))
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throw Error("Failed to parse pbsim2fa read names '" + qname + "'");
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s[2] = parseInt(s[2]);
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s[3] = parseInt(s[3]);
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s.shift(); // skip pbsim orginal read name
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if (mode == 0 || mode == 1) { // longest only or first only
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var max_i = 0;
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if (mode == 0) { // longest only
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var max = 0;
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for (var i = 0; i < a.length; ++i)
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if (a[i][5] > max)
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max = a[i][5], max_i = i;
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}
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var mapq = a[max_i][4];
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++tot[mapq];
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if (!is_correct(s, a[max_i])) {
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if (mapq >= err_out_q)
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print('E', qname, a[max_i].join("\t"));
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++err[mapq];
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}
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} else if (mode == 2) { // all primary mode
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var max_err_mapq = -1, max_mapq = 0, max_err_i = -1;
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if (cap_short_mapq) {
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var max = 0, max_q = 0;
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for (var i = 0; i < a.length; ++i)
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if (a[i][5] > max)
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max = a[i][5], max_q = a[i][4];
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for (var i = 0; i < a.length; ++i)
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a[i][4] = max_q < a[i][4]? max_q : a[i][4];
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}
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for (var i = 0; i < a.length; ++i) {
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max_mapq = max_mapq > a[i][4]? max_mapq : a[i][4];
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if (!is_correct(s, a[i]))
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if (a[i][4] > max_err_mapq)
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max_err_mapq = a[i][4], max_err_i = i;
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}
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if (max_err_mapq >= 0) {
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++tot[max_err_mapq], ++err[max_err_mapq];
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if (max_err_mapq >= err_out_q)
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print('E', qname, a[max_err_i].join("\t"));
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} else ++tot[max_mapq];
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}
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}
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var lineno = 0, last = null, a = [];
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while (file.readline(buf) >= 0) {
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var line = buf.toString();
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++lineno;
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if (line[0] != '@') {
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var t = line.split("\t");
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if (last != t[0]) {
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if (last != null) count_err(last, a, tot, err, mode);
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a = [], last = t[0];
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}
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if (t[4] == '+' || t[4] == '-') { // PAF
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if (/\ts1:i:\d+/.test(line) && !/\ts2:i:\d+/.test(line)) // secondary alignment in minimap2 PAF
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continue;
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var mapq = parseInt(t[11]);
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if (mapq > max_mapq) mapq = max_mapq;
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a.push([t[5], parseInt(t[7]), parseInt(t[8]), t[4], mapq, parseInt(t[9])]);
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}
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}
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}
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if (last != null) count_err(last, a, tot, err, mode);
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buf.destroy();
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file.close();
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var sum_tot = 0, sum_err = 0, q_out = -1, sum_tot2 = 0, sum_err2 = 0;
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for (var q = max_mapq; q >= 0; --q) {
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if (tot[q] == 0) continue;
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if (q_out < 0 || err[q] > 0) {
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if (q_out >= 0) print('Q', q_out, sum_tot, sum_err, (sum_err2/sum_tot2).toFixed(9));
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sum_tot = sum_err = 0, q_out = q;
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}
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sum_tot += tot[q], sum_err += err[q];
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sum_tot2 += tot[q], sum_err2 += err[q];
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}
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print('Q', q_out, sum_tot, sum_err, (sum_err2/sum_tot2).toFixed(9));
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