Update @gmod/bam and use conservative pairing

GMOD · Nov 6, 2018 · 4bb060d · 4bb060d
1 parent a461991
commit 4bb060d
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Showing 3 changed files with 7 additions and 6 deletions.
diff --git a/src/JBrowse/Store/SeqFeature/BAM.js b/src/JBrowse/Store/SeqFeature/BAM.js
@@ -251,7 +251,7 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
                             feat = pairCache[name]
                             if (feat && records[i].id() != feat.f1.id()) {
                                 feat.f2 = this._bamRecordToFeature(records[i])
-                                pairCache[name] = undefined
+                                delete pairCache[name]
                                 this.featureCache[name] = feat
                             }
                             else {

diff --git a/src/JBrowse/View/Track/Alignments2.js b/src/JBrowse/View/Track/Alignments2.js
@@ -147,6 +147,7 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
             var initial = new Promise((resolve, reject) => {
                 var reg = this.browser.view.visibleRegion()
                 var len = reg.end - reg.start
+                console.log(len)
                 const region = {
                     ref: this.refSeq.name,
                     start: Math.max( 0, reg.start ),
@@ -157,8 +158,8 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
                 region.end = region.end
 
                 this.store.getPairedRanges(region, range => {
-                    region.start = Math.max(0, range.min - len)
-                    region.end = range.max + len
+                    region.start = range.min
+                    region.end = range.max
                     this.store.getFeatures(region, function() {}, resolve, reject)
                 }, reject)
             }).then(() => {

diff --git a/yarn.lock b/yarn.lock
@@ -135,9 +135,9 @@
     arrify "^1.0.1"
 
 "@gmod/bam@^1.0.3":
-  version "1.0.5"
-  resolved "https://registry.yarnpkg.com/@gmod/bam/-/bam-1.0.5.tgz#9be15cfbe9ec7968ae37c00b02364842ba1581b1"
-  integrity sha512-qDompvuWDgb/ajWRBy6wL2LnxkP11YlYrfKmy8XPiZLvVDq8PLK4s87ssyCIF/Hbedt2iIX7WBT0in77du2U6g==
+  version "1.0.7"
+  resolved "https://registry.yarnpkg.com/@gmod/bam/-/bam-1.0.7.tgz#dc52d7fe769e739ad018cfdb210f837e10997c40"
+  integrity sha512-GDBvYppB+8iGnuffSozCb42KDpbEkcxuDi5sM4cuOThUSi9rVpCrt4qUT6P6/N/v2xXXiTKQNbA0/Q49Iz9RAQ==
   dependencies:
     "@gmod/bgzf-filehandle" "^1.2.1"
     buffer-crc32 "^0.2.13"