removed hla typing - not good enough

allenday · Oct 24, 2014 · ba3ab0c · ba3ab0c
1 parent 7a8019e
commit ba3ab0c
Showing 1 changed file with 0 additions and 42 deletions.
diff --git 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();
 	}
 }