126 lines
3.8 KiB
JavaScript
126 lines
3.8 KiB
JavaScript
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 colors = ["0,128,255", "255,0,0", "0,192,0"];
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function print_lines(a, fmt) {
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if (a.length == 0) return;
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if (fmt == "bed") {
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var n_pri = 0;
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for (var i = 0; i < a.length; ++i)
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if (a[i][9] == 0) ++n_pri;
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if (n_pri > 1) {
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for (var i = 0; i < a.length; ++i)
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if (a[i][9] == 0) a[i][9] = 1;
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} else if (n_pri == 0) {
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warn("Warning: " + a[0][0] + " doesn't have a primary alignment");
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}
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for (var i = 0; i < a.length; ++i) {
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a[i][9] = colors[a[i][9]];
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a[i].shift();
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print(a[i].join("\t"));
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}
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}
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a.length = 0;
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}
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function main(args) {
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var re = /(\d+)([MIDNSH])/g;
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var c, fmt = "bed", with_hdr = false, hdr_only = false, name = 'splice2bed', pos = null;
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while ((c = getopt(args, "Hhn:p:")) != null) {
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if (c == 'h') with_hdr = true;
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else if (c == 'p') pos = getopt.arg;
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else if (c == 'H') with_hdr = hdr_only = true;
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else if (c == 'n') name = getopt.arg;
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}
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if (getopt.ind == args.length && !hdr_only) {
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warn("Usage: k8 splice2bed.js [options] <in.paf>");
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exit(1);
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}
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if (with_hdr) {
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if (pos != null)
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print('browser position ' + pos);
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print('track name=' + name + ' useScore=1 visibility=2 itemRgb="On"');
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}
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if (hdr_only) return;
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var file = new File(args[getopt.ind]);
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var buf = new Bytes();
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var a = [];
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while (file.readline(buf) >= 0) {
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var line = buf.toString();
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if (line.charAt(0) == '@') continue; // skip SAM header lines
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var t = line.split("\t");
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if (t.length >= 12 && (t[4] == '+' || t[4] == '-')) {
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if (a.length && a[0][0] != t[0]) {
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print_lines(a, fmt);
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a = [];
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}
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var is_pri = false, cigar = null;
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for (var i = 12; i < t.length; ++i) {
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if (t[i].substr(0, 5) == 'cg:Z:') {
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cigar = t[i].substr(5);
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} else if (t[i].substr(0, 5) == 's2:i:') {
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is_pri = true;
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}
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}
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if (cigar == null) throw Error("missing CIGAR");
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var m, x0 = 0, x = 0, bs = [], bl = [];
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while ((m = re.exec(cigar)) != null) {
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if (m[2] == 'M' || m[2] == 'D') {
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x += parseInt(m[1]);
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} else if (m[2] == 'N') {
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bs.push(x0);
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bl.push(x - x0);
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x += parseInt(m[1]);
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x0 = x;
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}
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}
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bs.push(x0);
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bl.push(x - x0);
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a.push([t[0], t[5], t[7], t[8], t[0], Math.floor(t[9]/t[10]*1000), t[4], t[7], t[8], is_pri? 0:2, bs.length, bl.join(",")+",", bs.join(",")+","]);
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} else {
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throw Error("unrecognized input format");
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}
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}
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print_lines(a, fmt);
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buf.destroy();
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file.close();
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}
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main(arguments);
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