From: Colin <col...@gm...> - 2014-07-29 17:58:01
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Hi Dadu, I wanted to follow up with this, but I must apologize for the long wait. In a quick test, I found that I could add the ambiguous bases by changing this line ========= diff --git a/src/JBrowse/Store/SeqFeature/BAM/LazyFeature.js b/src/JBrowse/Store/SeqFeature/BAM/LazyFeature.js index d2ab8f7..07894ca 100644 --- a/src/JBrowse/Store/SeqFeature/BAM/LazyFeature.js +++ b/src/JBrowse/Store/SeqFeature/BAM/LazyFeature.js @@ -5,7 +5,7 @@ define( ['dojo/_base/array', ], function( array, Util, BAMUtil, SimpleFeature ) { -var SEQRET_DECODER = ['=', 'A', 'C', 'x', 'G', 'x', 'x', 'x', 'T', 'x', 'x', 'x', 'x', 'x', 'x', 'N']; +var SEQRET_DECODER = ['=', 'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N']; ========== You can also add these bases to be colored on the track by adding .base_w { } or other base types in sequence.css. -Colin On Thu, Jul 17, 2014 at 12:25 AM, Dadu <kha...@gm...> wrote: > Dear All, > > > I am unable to see the ambiguous base in JBrowse when i uploaded bam file > as a track. Instead of ambiguous base it display’s 'X' character . Can any > one tell me how do i configure to see ambiguous base instead of 'X'. > > Thanks and regards, > Dadu > > > ------------------------------------------------------------------------------ > Want fast and easy access to all the code in your enterprise? Index and > search up to 200,000 lines of code with a free copy of Black Duck > Code Sight - the same software that powers the world's largest code > search on Ohloh, the Black Duck Open Hub! Try it now. > http://p.sf.net/sfu/bds > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > |