move to a new project bwa-typeHLA
The two scripts cannot be used standalone anyway.
This commit is contained in:
Heng Li
parent
c2f2cb03ce
commit
4e97cdfde8
287
bwa-typeHLA.js
287
bwa-typeHLA.js
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@ -1,287 +0,0 @@
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/*****************************************************************
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* The K8 Javascript interpreter is required to run this script. *
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* *
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* Source code: https://github.com/attractivechaos/k8 *
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* Binary: http://sourceforge.net/projects/lh3/files/k8/ *
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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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*** Main function ***
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*********************/
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var c, thres_len = 50, thres_ratio = .8, thres_nm = 5, dbg = false;
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// parse command line options
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while ((c = getopt(arguments, "dl:n:")) != null) {
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if (c == 'l') thres_len = parseInt(getopt.arg);
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else if (c == 'n') thres_nm = parseInt(getopt.arg);
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else if (c == 'd') dbg = true;
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}
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if (arguments.length == getopt.ind) {
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print("");
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print("Usage: k8 bwa-typeHLA.js [options] <exon-to-contig.sam>\n");
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print("Options: -n INT drop a contig if the edit distance to the closest gene is >INT ["+thres_nm+"]");
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print(" -l INT drop a contig if its match too short ["+thres_len+"]");
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print("");
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print("Note: The output is TAB delimited with each line consisting of allele1, allele2,");
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print(" #mismatches/gaps on primary exons, #mismatches/gaps on other exons and");
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print(" #exons used in typing.\n");
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exit(1);
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}
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// read alignments
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var file = new File(arguments[getopt.ind]);
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var buf = new Bytes();
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var re_cigar = /(\d+)([MIDSH])/g;
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var len = {}, list = [], gcnt = [];
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while (file.readline(buf) >= 0) {
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var m, mm, line = buf.toString();
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var t = line.split("\t");
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// SAM header
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if (t[0].charAt(0) == '@') {
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if (t[0] == '@SQ' && (m = /LN:(\d+)/.exec(line)) != null && (mm = /SN:(\S+)/.exec(line)) != null)
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len[mm[1]] = parseInt(m[1]);
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continue;
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}
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// parse gene name and exon number
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var gene = null, exon = null;
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if ((m = /^(HLA-[^\s_]+)_(\d+)/.exec(t[0])) != null) {
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gene = m[1], exon = parseInt(m[2]) - 1;
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if (gcnt[exon] == null) gcnt[exon] = {};
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gcnt[exon][gene] = true;
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}
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if (gene == null || exon == null || t[2] == '*') continue;
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// parse clipping and aligned length
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var x = 0, ts = parseInt(t[3]) - 1, te = ts, clip = [0, 0];
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while ((m = re_cigar.exec(t[5])) != null) {
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var l = parseInt(m[1]);
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if (m[2] == 'M') x += l, te += l;
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else if (m[2] == 'I') x += l;
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else if (m[2] == 'D') te += l;
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else if (m[2] == 'S' || m[2] == 'H') clip[x==0?0:1] = l;
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}
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var tl = len[t[2]];
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var left = ts < clip[0]? ts : clip[0];
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var right = tl - te < clip[1]? tl - te : clip[1];
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var nm = (m = /\tNM:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 0;
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list.push([t[2], gene, exon, ts, te, nm, left + right]); // left+right should be 0 given a prefix-suffix alignment
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}
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buf.destroy();
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file.close();
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// identify the primary exons, the exons associated with most genes
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var pri_exon = [], n_pri_exons;
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{
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var cnt = [], max = 0;
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// count the number of genes per exon and track the max
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for (var e = 0; e < gcnt.length; ++e) {
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if (gcnt[e] != null) {
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var c = 0, h = gcnt[e];
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for (var x in h) ++c;
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cnt[e] = c;
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max = max > c? max : c;
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} else cnt[e] = 0;
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}
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// find primary exons
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var pri_list = [];
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for (var e = 0; e < cnt.length; ++e) {
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if (cnt[e] == max) pri_list.push(e + 1);
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pri_exon[e] = cnt[e] == max? 1 : 0;
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}
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warn("List of primary exons: ["+pri_list.join(",")+"]");
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n_pri_exons = pri_list.length;
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}
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// convert strings to integers (for performance)
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var ghash = {}, glist = [], chash = {}, clist = [], elist = [];
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for (var i = 0; i < list.length; ++i) {
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if (ghash[list[i][1]] == null) {
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ghash[list[i][1]] = glist.length;
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glist.push(list[i][1]);
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}
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if (chash[list[i][0]] == null) {
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chash[list[i][0]] = clist.length;
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clist.push(list[i][0]);
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}
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var g = ghash[list[i][1]];
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if (elist[g] == null) elist[g] = {};
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elist[g][list[i][2]] = true;
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}
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// reorganize hits to exons
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var exons = [];
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for (var i = 0; i < list.length; ++i) {
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var li = list[i];
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if (exons[li[2]] == null) exons[li[2]] = [];
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exons[li[2]].push([chash[li[0]], ghash[li[1]], li[5] + li[6], li[4] - li[3]]);
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}
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// initialize genotype scores
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var pair = [];
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for (var i = 0; i < glist.length; ++i) {
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pair[i] = [];
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for (var j = 0; j <= i; ++j)
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pair[i][j] = 0;
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}
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function update_pair(x, m, is_pri)
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{
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var y, z;
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y = (x>>14&0xff) + m < 0xff? (x>>14&0xff) + m : 0xff;
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if (is_pri) z = (x>>22) + m < 0xff? (x>>22) + m : 0xff;
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else z = x>>22;
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return z<<22 | y<<14 | ((x&0x3fff) + (1<<6|is_pri));
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}
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// type each exon
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var score = [], ctg = [];
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for (var e = 0; e < exons.length; ++e) {
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score[e] = []; ctg[e] = [];
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if (exons[e] == null) continue;
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var ee = exons[e], is_pri = pri_exon[e]? 1 : 0;
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// find contigs and genes associated with the current exon
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var ch = {}, gh = {};
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for (var i = 0; i < ee.length; ++i) {
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if (elist[ee[i][1]][e] != null)
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ch[ee[i][0]] = true, gh[ee[i][1]] = true;
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}
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var ga = [], ca = ctg[e];
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for (var c in ch) ca.push(parseInt(c));
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for (var g in gh) ga.push(parseInt(g));
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var named_ca = [];
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for (var i = 0; i < ca.length; ++i) named_ca.push(clist[ca[i]]);
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warn("Processing exon "+(e+1)+" (" +ga.length+ " genes; " +ca.length+ " contigs: [" +named_ca.join(", ")+ "])...");
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// set unmapped entries to high mismatch
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var sc = score[e];
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for (var k = 0; k < ga.length; ++k) {
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var g = ga[k];
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if (sc[g] == null) sc[g] = [];
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for (var i = 0; i < ca.length; ++i)
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sc[g][ca[i]] = 0xff;
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}
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// convert representation again
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var max_len = [];
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for (var i = 0; i < ee.length; ++i) {
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var c = ee[i][0], g = ee[i][1];
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sc[g][c] = sc[g][c] < ee[i][2]? sc[g][c] : ee[i][2];
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if (max_len[c] == null) max_len[c] = 0;
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max_len[c] = max_len[c] > ee[i][3]? max_len[c] : ee[i][3];
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}
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// drop mismapped contigs
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var max_max_len = 0;
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for (var k = 0; k < ca.length; ++k)
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max_max_len = max_max_len > max_len[ca[k]]? max_max_len : max_len[ca[k]];
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var dropped = [];
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for (var k = 0; k < ca.length; ++k) {
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var min = 0x7fffffff, c = ca[k];
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for (var i = 0; i < ga.length; ++i) {
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var g = ga[i];
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min = min < sc[g][c]? min : sc[g][c];
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}
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dropped[c] = min > thres_nm? true : false;
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if (max_len[c] < thres_len && max_len[c] < thres_ratio * max_max_len) dropped[c] = true;
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if (dropped[c]) warn("Dropped contig " +clist[c]+ " due to high divergence to all genes (minNM=" +min+ "; maxLen=" +max_len[c]+ ")");
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}
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// fill the pair array
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for (var i = 0; i < ga.length; ++i) {
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var m = 0, gi = ga[i], g1 = sc[gi];
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// homozygous
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for (var k = 0; k < ca.length; ++k) {
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var c = ca[k];
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if (!dropped[c]) m += g1[c];
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}
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pair[gi][gi] = update_pair(pair[gi][gi], m, is_pri);
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// heterozygous
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for (var j = i + 1; j < ga.length; ++j) {
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var gj = ga[j], g2 = sc[gj], m = 0, a = [0, 0];
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for (var k = 0; k < ca.length; ++k) {
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var c = ca[k];
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if (!dropped[c]) {
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m += g1[c] < g2[c]? g1[c] : g2[c];
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++a[g1[c]<g2[c]? 0:1];
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}
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}
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if (a[0] == 0 || a[1] == 0) m = 0xff; // if all contigs are assigned to one gene, it is not good
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if (gi < gj) pair[gj][gi] = update_pair(pair[gj][gi], m, is_pri);
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else pair[gi][gj] = update_pair(pair[gi][gj], m, is_pri);
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}
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}
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}
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// extract the 3rd and 4th digits
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var gsub = [], gsuf = [];
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for (var i = 0; i < glist.length; ++i) {
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var m = /^HLA-[^*\s]+\*\d+:(\d+).*([A-Z]?)$/.exec(glist[i]);
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gsub[i] = parseInt(m[1]);
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gsuf[i] = /[A-Z]$/.test(glist[i])? 1 : 0;
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}
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// genotyping
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var min_nm = 0x7fffffff;
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for (var i = 0; i < glist.length; ++i)
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for (var j = 0; j <= i; ++j)
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if ((pair[i][j]&63) == n_pri_exons)
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min_nm = min_nm < pair[i][j]>>14? min_nm : pair[i][j]>>14;
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var out = [];
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for (var i = 0; i < glist.length; ++i)
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for (var j = 0; j <= i; ++j)
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if ((pair[i][j]&63) == n_pri_exons && pair[i][j]>>14 <= min_nm + 1)
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out.push([pair[i][j]>>14, pair[i][j]>>6&0xff, i, j, (gsuf[i] + gsuf[j])<<16|(gsub[i] + gsub[j])]);
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out.sort(function(a, b) { return a[0]!=b[0]? a[0]-b[0] : a[1]!=b[1]? b[1]-a[1] : a[4]!=b[4]? a[4]-b[4] : a[2]!=b[2]? a[2]-b[2] : a[3]-b[3]});
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for (var i = 0; i < out.length; ++i) {
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print("GT", glist[out[i][3]], glist[out[i][2]], out[i][0]>>8&0xff, out[i][0]&0xff, out[i][1]);
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if (dbg) {
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var a1 = out[i][2], a2 = out[i][3];
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for (var e = 0; e < exons.length; ++e) {
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if (exons[e] == null) continue;
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if (elist[a1][e] == null || elist[a2][e] == null) continue;
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for (var k = 0; k < ctg[e].length; ++k) {
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var c = ctg[e][k];
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print("DB", e+1, score[e][a2][c], score[e][a1][c], clist[c]);
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}
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}
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}
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}
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@ -1,42 +0,0 @@
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#!/bin/bash
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is_ctg=0
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if [ $# -gt 1 ] && [ $1 == '-A' ]; then
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is_ctg=1
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shift
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fi
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if [ $# -lt 2 ]; then
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echo "Usage: $0 [-A] <prefix> <gene>"
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exit 1
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fi
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root=`dirname $0`
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pre=$1.$2
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# de novo assembly
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if [ $is_ctg -eq 0 ]; then
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len=`$root/seqtk comp $pre.fq | awk '{++x;y+=$2}END{printf("%.0f\n", y/x)}'`
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$root/fermi2.pl unitig -t2 -l$len -p $pre.tmp $pre.fq > $pre.tmp.mak
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make -f $pre.tmp.mak EXE_FERMI2=$root/fermi2 EXE_ROPEBWT2=$root/ropebwt2
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else
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rm -f $pre.tmp.mag.gz
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ln -s $pre.fq $pre.tmp.mag.gz
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fi
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# get contigs overlapping HLA exons
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(ls $root/HLA-idx/*.fa | xargs -i $root/bwa mem -t2 -B1 -O1 -E1 {} $pre.tmp.mag.gz 2>/dev/null) | grep -v ^@ | sort -k3,3 -k4,4n | bgzip > $pre.tmp.sam.gz
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$root/tabix -Bpsam $pre.tmp.sam.gz $root/HLA-approx.anno | cut -f1 | sort | uniq > $pre.tmp.kept
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gzip -dc $pre.tmp.sam.gz | perl -ane 'print if $F[5]!~/^\d+[SH]/ && $F[5]!~/[SH]$/ && /AS:i:(\d+).*XS:i:(\d+)/ && $1==$2' | cut -f1 | sort | uniq > $pre.tmp.dropped
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awk -v f=$pre.tmp.dropped 'BEGIN{while((getline<f)>0)l[$1]=1}!l[$1]' $pre.tmp.kept | $root/seqtk subseq $pre.tmp.mag.gz - | gzip -1 > $pre.tmp.fq.gz
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# map HLA exons to de novo contigs
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$root/bwa index -p $pre.tmp $pre.tmp.fq.gz 2>/dev/null
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$root/bwa mem -aD.1 -t2 $pre.tmp $root/hla.fa 2>/dev/null | egrep "^(@|$2)" > $pre.sam
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# type HLA
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$root/k8 $root/bwa-typeHLA.js $pre.sam > $pre.gt
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# delete temporary files
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rm -f $pre.tmp.*
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