Commit 8cce9045 authored by Mathieu Giraud's avatar Mathieu Giraud

js/{model,clone}.js: clone.getRawReads(), bypass normalization

see #3662 and #3650.
parent de61fc3f
......@@ -688,21 +688,25 @@ Clone.prototype = {
},
/* compute the clone reads number ( sum of all reads of clones clustered )
* @t : tracking point (default value : current tracking point)
* @time : tracking point (default value : current tracking point)
* @raw: do not normalize
* */
getReads: function (time) {
getReads: function (time, raw) {
time = this.m.getTime(time)
var result = 0;
var cluster = this.getCluster()
for (var j = 0; j < cluster.length; j++) {
result += this.m.normalize_reads(this.m.clone(cluster[j]), time);
result += this.m.normalize_reads(this.m.clone(cluster[j]), time, raw);
}
return result
}, //end getSize
},
getRawReads: function (time) {
return this.getReads(time, true)
},
/* return a list of read numbers (sum of all reads of clustered clones) for all samples
* */
......
......@@ -689,10 +689,11 @@ changeAlleleNotation: function(alleleNotation) {
},
/**
* normalize a number of reads
* normalize a number of reads according to this.NORM_EXTERNAL
* if raw is defined, do not normalize
*/
normalize_reads: function(clone, time) {
if (this.normalization_mode == this.NORM_EXTERNAL && clone.normalized_reads != undefined) {
normalize_reads: function(clone, time, raw) {
if (this.normalization_mode == this.NORM_EXTERNAL && clone.normalized_reads != undefined && !(raw != undefined)) {
return clone.normalized_reads[time] ;
} else {
return clone.reads[time] ;
......
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