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Clean up junction alignment HTML output #31

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Properly account for shifts in junction endpoints since it was first identified.

Leave out the vertical bars showing where the overlap originally was. Instead 
draw the overlap on both sides, but dim it (by using low quality bases or a 
special color code) on the side where it was "removed".

The position send to the aligner should be the inserted bases if overlap is 
negative or the insert position between the two ends if the overlap was 
resolved to zero.

Eventually, we should calculate numbers showing the number of reads supporting 
the old junction and the new junction using reads that span these bases.

Original issue reported on code.google.com by jeffrey....@gmail.com on 15 Nov 2011 at 5:23

GoogleCodeExporter commented 8 years ago 
The way we draw alignments, it is not possible to put a vertical bar between 
two bases.  Right now I'm able to only show vertical bars if there's negative 
overlap (insertion).

Original comment by MDStr...@gmail.com on 18 Nov 2011 at 1:13

GoogleCodeExporter commented 8 years ago 
Matt fixed this a while back. Very nice!

Original comment by jeffrey....@gmail.com on 5 Feb 2012 at 8:16