index.html does not agree with output.gd

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Breseq run on REL11008
2. compare predicted mutation on index.html at 16,975 to output.gd at same 
location

What is the expected output? What do you see instead?
Expect index.html to show -14bp deletion associated with IS150 insertion. 

What version of the product are you using? On what operating system?
revision c633c5005425 lonestar

Please provide any additional information below.
Not sure if it is related, but the first unassigned missing coverage evidence 
is the missing coverage associated with the 14bp deletion at this location 
after IS150 inserts. Might be related to issue 55? Biggest difference is this 
predicts the deletion as part of the insertion rather than 2 insertions 
followed by a deletion.

Original issue reported on code.google.com by Daniel.D...@gmail.com on 19 Sep 2012 at 6:23

Attachments:

• REL11008_output.tar.gz

[GoogleCodeExporter]

Edge case: This is apparently two new IS insertions near each other and a 
deletion between them that only got rid of 14 base pairs. The threshold for 
negative duplications needs to be made more stringent and the related 
improvement to predict IS insertions + IS mediated deletions needs to be added 
to completely get this predicted.

Original comment by jeffrey....@gmail.com on 19 Sep 2012 at 7:14

[GoogleCodeExporter]

Fixed so MC goes with junction prediction.

Original comment by jeffrey....@gmail.com on 23 Dec 2012 at 5:29

• Changed state: Fixed

[GoogleCodeExporter]

This issue was closed by revision b69f14326a72.

Original comment by jeffrey....@gmail.com on 23 Dec 2012 at 5:29