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Alignments2 mate highlight fix #986

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merged 7 commits into from Feb 28, 2018
Merged

Alignments2 mate highlight fix #986

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820bfb4
add new function next_segment_position_highlight to return a location…
rdhayes Feb 13, 2018
df37cf7
update mate pair menu items to configure a highlight at the new next_…
rdhayes Feb 13, 2018
49c6582
remove dangling comma in a list
rdhayes Feb 13, 2018
0420eae
Merge branch 'dev' into Alignments2_mateHighlightFix
rbuels Feb 27, 2018
e4a4c7b
actually, it turned out to really be as simple as adding 1 to the pos…
rbuels Feb 27, 2018
f551271
update release notes
rbuels Feb 27, 2018
3b409b7
add comment about the next_segment_position being a locstring [skip ci]
rbuels Feb 28, 2018
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4 changes: 4 additions & 0 deletions release-notes.txt
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Expand Up @@ -56,6 +56,10 @@
* Fixed a security issue with JBrowse error messages. Thanks to @GrainGenes for
noticing and reporting it! (issue #602, @rbuels)

* Fixed an off-by-one error in the "Next segment position" field of BAM features.
Thanks to @keiranmraine for reporting it, and @rdhayes for tracking down the fix!
(issue #907, pull #986, @rdhayes)

* Fixed the broken demo track data source in the modENCODE sample data. Thanks
to @cmdcolin for the fix! (pull #999, @cmdcolin)

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4 changes: 3 additions & 1 deletion src/JBrowse/Store/SeqFeature/BAM/LazyFeature.js
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Expand Up @@ -208,9 +208,11 @@ var Feature = Util.fastDeclare(
return cigar;
},
next_segment_position: function() {
// NOTE: next_segment_position is a JBrowse location string, so
// it is in 1-based coordinates. Thus, we add 1 to the position.
var nextSegment = this.file.indexToChr[this._get('_next_refid')];
if( nextSegment )
return nextSegment.name+':'+this._get('_next_pos');
return nextSegment.name+':'+(parseInt(this._get('_next_pos'))+1);
else
return undefined;
},
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