merged intron-eval into paftools
This commit is contained in:
Heng Li
parent
2025a6279a
commit
642af5591e
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@ -1,267 +0,0 @@
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/*******************************
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* Command line option parsing *
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*******************************/
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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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/***********************
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* Interval operations *
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***********************/
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Interval = {};
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Interval.sort = function(a)
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{
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if (typeof a[0] == 'number')
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a.sort(function(x, y) { return x - y });
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else a.sort(function(x, y) { return x[0] != y[0]? x[0] - y[0] : x[1] - y[1] });
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}
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Interval.merge = function(a, sorted)
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{
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if (typeof sorted == 'undefined') sorted = true;
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if (!sorted) Interval.sort(a);
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var k = 0;
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for (var i = 1; i < a.length; ++i) {
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if (a[k][1] >= a[i][0])
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a[k][1] = a[k][1] > a[i][1]? a[k][1] : a[i][1];
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else a[++k] = a[i].slice(0);
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}
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a.length = k + 1;
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}
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Interval.index_end = function(a, sorted)
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{
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if (a.length == 0) return;
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if (typeof sorted == 'undefined') sorted = true;
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if (!sorted) Interval.sort(a);
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a[0].push(0);
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var k = 0, k_en = a[0][1];
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for (var i = 1; i < a.length; ++i) {
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if (k_en <= a[i][0]) {
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for (++k; k < i; ++k)
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if (a[k][1] > a[i][0])
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break;
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k_en = a[k][1];
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}
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a[i].push(k);
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}
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}
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Interval.find_intv = function(a, x)
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{
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var left = -1, right = a.length;
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if (typeof a[0] == 'number') {
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while (right - left > 1) {
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var mid = left + ((right - left) >> 1);
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if (a[mid] > x) right = mid;
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else if (a[mid] < x) left = mid;
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else return mid;
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}
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} else {
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while (right - left > 1) {
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var mid = left + ((right - left) >> 1);
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if (a[mid][0] > x) right = mid;
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else if (a[mid][0] < x) left = mid;
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else return mid;
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}
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}
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return left;
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}
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Interval.find_ovlp = function(a, st, en)
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{
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if (a.length == 0 || st >= en) return [];
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var l = Interval.find_intv(a, st);
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var k = l < 0? 0 : a[l][a[l].length - 1];
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var b = [];
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for (var i = k; i < a.length; ++i) {
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if (a[i][0] >= en) break;
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else if (st < a[i][1])
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b.push(a[i]);
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}
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return b;
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}
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/*****************
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* Main function *
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*****************/
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var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false;
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while ((c = getopt(arguments, "l:ep")) != null) {
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if (c == 'l') l_fuzzy = parseInt(getopt.arg);
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else if (c == 'e') print_err_only = print_ovlp = true;
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else if (c == 'p') print_ovlp = true;
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}
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if (arguments.length - getopt.ind < 2) {
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print("Usage: k8 intron-eval.js [options] <gene.gtf> <aln.sam>");
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exit(1);
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}
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var file, buf = new Bytes();
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var tr = {};
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file = new File(arguments[getopt.ind]);
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while (file.readline(buf) >= 0) {
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var m, t = buf.toString().split("\t");
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if (t[0].charAt(0) == '#') continue;
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if (t[2] != 'exon') continue;
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var st = parseInt(t[3]) - 1;
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var en = parseInt(t[4]);
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if ((m = /transcript_id "(\S+)"/.exec(t[8])) == null) continue;
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var tid = m[1];
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if (tr[tid] == null) tr[tid] = [t[0], t[6], 0, 0, []];
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tr[tid][4].push([st, en]);
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}
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file.close();
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var anno = {};
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for (var tid in tr) {
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var t = tr[tid];
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Interval.sort(t[4]);
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t[2] = t[4][0][0];
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t[3] = t[4][t[4].length - 1][1];
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if (anno[t[0]] == null) anno[t[0]] = [];
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var s = t[4];
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for (var i = 0; i < s.length - 1; ++i) {
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if (s[i][1] >= s[i+1][0])
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warn("WARNING: incorrect annotation for transcript "+tid+" ("+s[i][1]+" >= "+s[i+1][0]+")")
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anno[t[0]].push([s[i][1], s[i+1][0]]);
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}
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}
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tr = null;
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for (var chr in anno) {
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var e = anno[chr];
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if (e.length == 0) continue;
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Interval.sort(e);
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var k = 0;
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for (var i = 1; i < e.length; ++i) // dedup
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if (e[i][0] != e[k][0] || e[i][1] != e[k][1])
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e[++k] = e[i].slice(0);
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e.length = k + 1;
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Interval.index_end(e);
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}
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var n_pri = 0, n_unmapped = 0, n_mapped = 0;
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var n_sgl = 0, n_splice = 0, n_splice_hit = 0, n_splice_novel = 0;
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file = new File(arguments[getopt.ind+1]);
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var last_qname = null;
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var re_cigar = /(\d+)([MIDNSHX=])/g;
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while (file.readline(buf) >= 0) {
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var m, t = buf.toString().split("\t");
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if (t[0].charAt(0) == '@') continue;
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var flag = parseInt(t[1]);
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if (flag&0x100) continue;
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if (first_only && last_qname == t[0]) continue;
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if (t[2] == '*') {
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++n_unmapped;
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continue;
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} else {
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++n_pri;
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if (last_qname != t[0]) ++n_mapped;
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}
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var pos = parseInt(t[3]) - 1, intron = [];
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while ((m = re_cigar.exec(t[5])) != null) {
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var len = parseInt(m[1]), op = m[2];
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if (op == 'N') {
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intron.push([pos, pos + len]);
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pos += len;
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} else if (op == 'M' || op == 'X' || op == '=' || op == 'D') pos += len;
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}
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if (intron.length == 0) {
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++n_sgl;
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continue;
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}
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n_splice += intron.length;
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var chr = anno[t[2]];
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if (chr != null) {
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for (var i = 0; i < intron.length; ++i) {
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var o = Interval.find_ovlp(chr, intron[i][0], intron[i][1]);
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if (o.length > 0) {
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var hit = false;
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for (var j = 0; j < o.length; ++j) {
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var st_diff = intron[i][0] - o[j][0];
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var en_diff = intron[i][1] - o[j][1];
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if (st_diff < 0) st_diff = -st_diff;
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if (en_diff < 0) en_diff = -en_diff;
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if (st_diff <= l_fuzzy && en_diff <= l_fuzzy)
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++n_splice_hit, hit = true;
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if (hit) break;
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}
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if (print_ovlp) {
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var type = hit? 'C' : 'P';
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if (hit && print_err_only) continue;
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var x = '[';
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for (var j = 0; j < o.length; ++j) {
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if (j) x += ', ';
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x += '(' + o[j][0] + "," + o[j][1] + ')';
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}
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x += ']';
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print(type, t[0], i+1, t[2], intron[i][0], intron[i][1], x);
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}
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} else {
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++n_splice_novel;
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if (print_ovlp)
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print('N', t[0], i+1, t[2], intron[i][0], intron[i][1]);
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}
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}
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} else {
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n_splice_novel += intron.length;
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}
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last_qname = t[0];
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}
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file.close();
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buf.destroy();
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if (!print_ovlp) {
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print("# unmapped reads: " + n_unmapped);
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print("# mapped reads: " + n_mapped);
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print("# primary alignments: " + n_pri);
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print("# singletons: " + n_sgl);
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print("# predicted introns: " + n_splice);
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print("# non-overlapping introns: " + n_splice_novel);
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print("# correct introns: " + n_splice_hit + " (" + (n_splice_hit / n_splice * 100).toFixed(2) + "%)");
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}
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152
misc/paftools.js
152
misc/paftools.js
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@ -1262,6 +1262,156 @@ function paf_pbsim2fq(args)
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buf2.destroy();
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}
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function paf_junceval(args) // FIXME: the reported number of mapped reads is slightly off
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{
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var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false;
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while ((c = getopt(args, "l:ep")) != null) {
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if (c == 'l') l_fuzzy = parseInt(getopt.arg);
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else if (c == 'e') print_err_only = print_ovlp = true;
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else if (c == 'p') print_ovlp = true;
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}
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if (args.length - getopt.ind < 2) {
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print("Usage: paftools.js junceval [options] <gene.gtf> <aln.sam>");
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print("Options:");
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print(" -l INT tolerance of junction positions (0 for exact) [0]");
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print(" -p print overlapping introns");
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print(" -e print erroreous overlapping introns");
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exit(1);
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}
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var file, buf = new Bytes();
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var tr = {};
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file = new File(args[getopt.ind]);
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while (file.readline(buf) >= 0) {
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var m, t = buf.toString().split("\t");
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if (t[0].charAt(0) == '#') continue;
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if (t[2] != 'exon') continue;
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var st = parseInt(t[3]) - 1;
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var en = parseInt(t[4]);
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if ((m = /transcript_id "(\S+)"/.exec(t[8])) == null) continue;
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var tid = m[1];
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if (tr[tid] == null) tr[tid] = [t[0], t[6], 0, 0, []];
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tr[tid][4].push([st, en]);
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}
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file.close();
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var anno = {};
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for (var tid in tr) {
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var t = tr[tid];
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Interval.sort(t[4]);
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t[2] = t[4][0][0];
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t[3] = t[4][t[4].length - 1][1];
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if (anno[t[0]] == null) anno[t[0]] = [];
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var s = t[4];
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for (var i = 0; i < s.length - 1; ++i) {
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if (s[i][1] >= s[i+1][0])
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warn("WARNING: incorrect annotation for transcript "+tid+" ("+s[i][1]+" >= "+s[i+1][0]+")")
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anno[t[0]].push([s[i][1], s[i+1][0]]);
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}
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}
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tr = null;
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for (var chr in anno) {
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var e = anno[chr];
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if (e.length == 0) continue;
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Interval.sort(e);
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var k = 0;
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for (var i = 1; i < e.length; ++i) // dedup
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if (e[i][0] != e[k][0] || e[i][1] != e[k][1])
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e[++k] = e[i].slice(0);
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e.length = k + 1;
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Interval.index_end(e);
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}
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var n_pri = 0, n_unmapped = 0, n_mapped = 0;
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var n_sgl = 0, n_splice = 0, n_splice_hit = 0, n_splice_novel = 0;
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file = new File(args[getopt.ind+1]);
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var last_qname = null;
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var re_cigar = /(\d+)([MIDNSHX=])/g;
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while (file.readline(buf) >= 0) {
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var m, t = buf.toString().split("\t");
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if (t[0].charAt(0) == '@') continue;
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var flag = parseInt(t[1]);
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if (flag&0x100) continue;
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if (first_only && last_qname == t[0]) continue;
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if (t[2] == '*') {
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++n_unmapped;
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continue;
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} else {
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++n_pri;
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if (last_qname != t[0]) ++n_mapped;
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}
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var pos = parseInt(t[3]) - 1, intron = [];
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while ((m = re_cigar.exec(t[5])) != null) {
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var len = parseInt(m[1]), op = m[2];
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if (op == 'N') {
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intron.push([pos, pos + len]);
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pos += len;
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} else if (op == 'M' || op == 'X' || op == '=' || op == 'D') pos += len;
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}
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if (intron.length == 0) {
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++n_sgl;
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continue;
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}
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n_splice += intron.length;
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var chr = anno[t[2]];
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if (chr != null) {
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for (var i = 0; i < intron.length; ++i) {
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var o = Interval.find_ovlp(chr, intron[i][0], intron[i][1]);
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if (o.length > 0) {
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var hit = false;
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for (var j = 0; j < o.length; ++j) {
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var st_diff = intron[i][0] - o[j][0];
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var en_diff = intron[i][1] - o[j][1];
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if (st_diff < 0) st_diff = -st_diff;
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if (en_diff < 0) en_diff = -en_diff;
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if (st_diff <= l_fuzzy && en_diff <= l_fuzzy)
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++n_splice_hit, hit = true;
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if (hit) break;
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}
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if (print_ovlp) {
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var type = hit? 'C' : 'P';
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if (hit && print_err_only) continue;
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var x = '[';
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for (var j = 0; j < o.length; ++j) {
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if (j) x += ', ';
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x += '(' + o[j][0] + "," + o[j][1] + ')';
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}
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x += ']';
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print(type, t[0], i+1, t[2], intron[i][0], intron[i][1], x);
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}
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} else {
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++n_splice_novel;
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if (print_ovlp)
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print('N', t[0], i+1, t[2], intron[i][0], intron[i][1]);
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}
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}
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} else {
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n_splice_novel += intron.length;
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}
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last_qname = t[0];
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}
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file.close();
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buf.destroy();
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if (!print_ovlp) {
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print("# unmapped reads: " + n_unmapped);
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print("# mapped reads: " + n_mapped);
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print("# primary alignments: " + n_pri);
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print("# singletons: " + n_sgl);
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print("# predicted introns: " + n_splice);
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print("# non-overlapping introns: " + n_splice_novel);
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print("# correct introns: " + n_splice_hit + " (" + (n_splice_hit / n_splice * 100).toFixed(2) + "%)");
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}
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}
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// evaluate overlap sensitivity
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function paf_ov_eval(args)
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{
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@ -1354,6 +1504,7 @@ function main(args)
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|||
print(" mapeval evaluate mapping accuracy using mason2/PBSIM-simulated FASTQ");
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print(" mason2fq convert mason2-simulated SAM to FASTQ");
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print(" pbsim2fq convert PBSIM-simulated MAF to FASTQ");
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||||
print(" junceval evaluate splice junction consistency with known annotations");
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||||
print(" ov-eval evaluate read overlap sensitivity using read-to-ref mapping");
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exit(1);
|
||||
}
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||||
|
|
@ -1368,6 +1519,7 @@ function main(args)
|
|||
else if (cmd == 'mapeval') paf_mapeval(args);
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||||
else if (cmd == 'mason2fq') paf_mason2fq(args);
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||||
else if (cmd == 'pbsim2fq') paf_pbsim2fq(args);
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||||
else if (cmd == 'junceval') paf_junceval(args);
|
||||
else if (cmd == 'ov-eval') paf_ov_eval(args);
|
||||
else throw Error("unrecognized command: " + cmd);
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue