From d19cf206ce5aed7eba211ac4b8606e93664a3082 Mon Sep 17 00:00:00 2001 From: Colin Date: Fri, 9 Nov 2018 10:09:22 -0500 Subject: [PATCH] Enable insert size coloring on normal alignments track --- src/JBrowse/Store/SeqFeature/BAM.js | 1 + src/JBrowse/Store/SeqFeature/_InsertSizeCache.js | 4 ++-- src/JBrowse/View/Track/Alignments2.js | 4 ++-- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/src/JBrowse/Store/SeqFeature/BAM.js b/src/JBrowse/Store/SeqFeature/BAM.js index 0e4d80dd39..0076f72fbe 100644 --- a/src/JBrowse/Store/SeqFeature/BAM.js +++ b/src/JBrowse/Store/SeqFeature/BAM.js @@ -222,6 +222,7 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In .then(records => { if(query.viewAsPairs) { const recs = records.map(f => this._bamRecordToFeature(f)) + recs.forEach(r => this.insertSizeCache.insertFeat(r)) this.pairFeatures(query, recs, featCallback, endCallback, errorCallback) } else { for(let i = 0; i < records.length; i++) { diff --git a/src/JBrowse/Store/SeqFeature/_InsertSizeCache.js b/src/JBrowse/Store/SeqFeature/_InsertSizeCache.js index e032f7744b..c260c5945d 100644 --- a/src/JBrowse/Store/SeqFeature/_InsertSizeCache.js +++ b/src/JBrowse/Store/SeqFeature/_InsertSizeCache.js @@ -24,14 +24,14 @@ return declare(null, { }, insertFeat(feat) { - this.featureCache[feat.get('name')] = feat + this.featureCache[feat.get('name')] = Math.abs(feat.get('template_length')) }, getInsertSizeStats() { if(Object.keys(this.featureCache).length > this.insertStatsCacheMin) { var total = Object.keys(this.featureCache).length var tlens = Object.entries(this.featureCache) - .map(([k, v]) => Math.abs(v.get('template_length'))) + .map(([k, v]) => Math.abs(v)) .filter(tlen => tlen < this.insertMaxSize) .sort((a, b) => a - b) var sum = tlens.reduce((a, b) => a + b, 0) diff --git a/src/JBrowse/View/Track/Alignments2.js b/src/JBrowse/View/Track/Alignments2.js index 2d7360afbf..bb13fb4dc5 100644 --- a/src/JBrowse/View/Track/Alignments2.js +++ b/src/JBrowse/View/Track/Alignments2.js @@ -61,12 +61,12 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], { var m = { type: 'dijit/Menu', - label: 'Pair options', + label: 'Track visualization options', children: [] } var c = { type: 'dijit/Menu', - label: 'Color options', + label: 'Coloring options', children: [] }