diff --git a/bwa-postalt.js b/bwa-postalt.js index 7292856..3a71cde 100644 --- a/bwa-postalt.js +++ b/bwa-postalt.js @@ -203,42 +203,6 @@ function parse_hit(s, opt) return h; } -function type_hla(w) -{ - var hla = ["A", "B", "C", "DQA1", "DQB1", "DRB1"]; - var hla_hash = {}, a = [], r = []; - for (var i = 0; i < hla.length; ++i) { - hla_hash[hla[i]] = i; - a[i] = []; - } - for (var i = 0; i < w.length; ++i) { - var t = w[i][0].split(/[:\*]/); - var x = hla_hash[t[0]]; - if (x != null) - a[x].push([w[i][0], t[1], t[1] + ':' + t[2], w[i][1]]); - } - for (var k = 1; k <= 2; ++k) { - for (var i = 0; i < hla.length; ++i) { - var ai = a[i], m = {}; - for (var j = 0; j < ai.length; ++j) { - var key = ai[j][k], val = ai[j][3]; - if (m[key] == null) m[key] = [-1, -1.0]; - if (m[key][1] < val) m[key] = [j, val]; - } - var sum = 0; - for (var x in m) sum += m[x][1]; - var max = -1, max2 = -1, max3 = -1, max_x, max_x2, max_x3; - for (var x in m) { - if (max < m[x][1]) max3 = max2, max_x3 = max_x2, max2 = max, max_x2 = max_x, max = m[x][1], max_x = x; - else if (max2 < m[x][1]) max3 = max2, max_x3 = max_x2, max2 = m[x][1], max_x2 = x; - else if (max3 < m[x][1]) max3 = m[x][1], max_x3 = x; - } - r.push([hla[i], k, hla[i]+'*'+max_x, max.toFixed(3), hla[i]+'*'+max_x2, max2.toFixed(3), hla[i]+'*'+max_x3, max3.toFixed(3)]); - } - } - return r; -} - function bwa_postalt(args) { var c, opt = { a:1, b:4, o:6, e:1, verbose:3, show_pri:false, update_mapq:true, min_mapq:10, min_sc:90, max_nm_sc:10, show_ev:false, min_pa_ratio:1 }; @@ -626,12 +590,6 @@ function bwa_postalt(args) fpout.write(weight_arr[i].join("\t") + '\n'); } fpout.close(); - - var r = type_hla(weight_hla); - fpout = new File(opt.pre + '.hla', "w"); - for (var i = 0; i < r.length; ++i) - fpout.write(r[i].join("\t") + '\n'); - fpout.close(); } }