Remove vestigial BAM code

GMOD · Sep 21, 2018 · cff7a88 · cff7a88
1 parent 070b0fc
commit cff7a88
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Showing 7 changed files with 5 additions and 1,229 deletions.
diff --git a/src/JBrowse/Model/BAIIndex.js b/src/JBrowse/Model/BAIIndex.js
diff --git a/src/JBrowse/Model/CSIIndex.js b/src/JBrowse/Model/CSIIndex.js
@@ -3,21 +3,16 @@ define([
            'JBrowse/Util',
            'JBrowse/Model/DataView',
            'JBrowse/Model/TabixIndex',
-           'JBrowse/Model/BGZip/VirtualOffset',
-           'JBrowse/Store/SeqFeature/BAM/Util'
+           'JBrowse/Model/BGZip/VirtualOffset'
        ],
        function(
            declare,
            Util,
            jDataView,
            TabixIndex,
-           VirtualOffset,
-           BAMUtil
+           VirtualOffset
        ) {
 
-var readInt   = BAMUtil.readInt;
-var readVirtualOffset = BAMUtil.readVirtualOffset;
-
 
 function lshift(num, bits) {
     return num * Math.pow(2, bits);

diff --git a/src/JBrowse/Store/SeqFeature/BAM.js b/src/JBrowse/Store/SeqFeature/BAM.js
@@ -21,7 +21,7 @@ class BamSlightlyLazyFeature {
     _get_cigar() { return this.record.get('cigar')}
     _get_seq_id() { return this._store._refIdToName(this.record.sequenceId)}
     _get_qc_failed() { return this.record.isFailedQc()}
-    _get_secondary_alignment() { return this.record.isSecondary()}
+    _get_secondary_alignment() { console.log('here',this.record.isSecondary());return this.record.isSecondary()}
     _get_supplementary_alignment() { return this.record.isSupplementary()}
     _get_multi_segment_template() { return this.record.isPaired()}
     _get_multi_segment_all_correctly_aligned() { return this.record.isProperlyPaired()}