Add function for pair orientation

GMOD · Oct 31, 2018 · d7a54a7 · d7a54a7
1 parent 7e6a28a
commit d7a54a7
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Showing 4 changed files with 2 additions and 2 deletions.
diff --git a/docs/tutorial/data_files/volvox-sv.bam b/docs/tutorial/data_files/volvox-sv.bam
diff --git a/docs/tutorial/data_files/volvox-sv.bam.bai b/docs/tutorial/data_files/volvox-sv.bam.bai
diff --git a/docs/tutorial/data_files/volvox-sv.bam.conf b/docs/tutorial/data_files/volvox-sv.bam.conf
@@ -2,7 +2,7 @@
 style.height = 7
 key = BAM - volvox-sv.bam
 storeClass = JBrowse/Store/SeqFeature/BAM
-urlTemplate = ../../raw/volvox/volvox-sv.sorted.bam
+urlTemplate = ../../raw/volvox/volvox-sv.bam
 viewAsPairs = true
 glyph = JBrowse/View/FeatureGlyph/PairedAlignment
 maxFeatureScreenDensity = 4

diff --git a/src/JBrowse/Store/SeqFeature/BAM.js b/src/JBrowse/Store/SeqFeature/BAM.js
@@ -56,6 +56,7 @@ class BamSlightlyLazyFeature {
     _get_multi_segment_first() { return this.record.isRead1()}
     _get_multi_segment_last() { return this.record.isRead2()}
     _get_multi_segment_next_segment_reversed() { return this.record.isMateReverseComplemented()}
+    _get_pair_orientation() { return this.record.getPairOrientation()}
     _get_unmapped() { return this.record.isSegmentUnmapped()}
     _get_next_seq_id() { return this._store._refIdToName(this.record._next_refid()) }
     _get_next_segment_position() { return this.record.isPaired()
@@ -292,7 +293,6 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
                             featCallback(feat)
                         }
                     }
-                    console.log(Object.keys(this.featureCache).length)
                     Object.entries(this.featureCache).forEach(([k, v]) => {
                         if(v._get('end') - v._get('start') < 1000000 && (v._get('end') > query.start && v._get('start') < query.end)) {
                             featCallback(v)