Incorrect call of IS3 mediated deletion

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What steps will reproduce the problem?
1. Run breseq on REL2038 (RS0009_TemperatureEvolved/REL2038.gd for files)
2. Run breseq apply on .gd output (I have edited the .gd file in RS0009 to 
correct for the issue)
3. Rerun breseq using the applied version as reference.

What is the expected output? What do you see instead?
1. Initial run predicts a 32,855 bp deletion at 1,409,784 mediated by IS3. 
Missing coverage size is predicted to be between 32854 and 34084 bases.
2. Apply runs correctly.
3. Breseq now predicts a 2bp insertion at 1,396,220.

The 2 bp inserting are identical to the last 2 bp of the original junction 
predicted in 1. If you run apply with a 32,853bp deletion 0 new mutations are 
predicted.

What version of the product are you using? On what operating system?
Running on ranger, 1. was run most recently on 1-17 with breseq  version 0.16  
revision a29663e2f17b; 2. was run most recently on 1-18; 3. was run most 
recently on 1-18 with breseq  version 0.16  revision 16dd19d0d1f1; and apply & 
re-breseq run with 32853bp deletion was run on 1-22 with breseq  version 0.16  
revision df0ca12577bc. 

Please provide any additional information below.
daniel.deatherage@gmail.com if anything isn't clear.

Original issue reported on code.google.com by Daniel.D...@gmail.com on 23 Jan 2012 at 4:44

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Did we fix this prediction?

Original comment by jeffrey....@gmail.com on 5 Feb 2012 at 8:20

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Working on this one. Due to assuming that junction ends flush with the end of a 
repeat region.

Original comment by jeffrey....@gmail.com on 12 Jun 2012 at 3:09

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I'm working on this.

Original comment by jeffrey....@gmail.com on 22 Jun 2012 at 2:07

• Changed state: Accepted

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Fixed.

Original comment by jeffrey....@gmail.com on 22 Jun 2012 at 9:17

• Changed state: Fixed