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gatk3的最后一个经典版本3.8
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Valentin Ruano-Rubio 84711b8e90 Fixed bug using GraphBased due to infinite likelihoods resulting from the calculation of alignment cost of very long insertion or deletions (done in linear scale) 
Stories:

  https://www.pivotaltracker.com/story/show/66263868

Bug:

  The problem was due to the way we were calculating the fix penalty of a large deletion or insertion. In this case we calculate the alignment likelihood of the portion
  or read or haplotype deletion as the penalty of that deletion/insertion without going through the full pair-hmm process. For large events this resulted in a 0 in
  in linear scale computations that ins transformed into an infinity in log scale.

Changes:

  - Change to use log10 scale for calculate those penalties.
  - Minor addition of .gitignore to hide ./public/external-example/target which is generated by the building process.
 		2014-04-01 16:14:52 -04:00
licensing deleted old license files 2013-07-02 16:36:47 -04:00
protected Fixed bug using GraphBased due to infinite likelihoods resulting from the calculation of alignment cost of very long insertion or deletions (done in linear scale) 2014-04-01 16:14:52 -04:00
public Fixed bug using GraphBased due to infinite likelihoods resulting from the calculation of alignment cost of very long insertion or deletions (done in linear scale) 2014-04-01 16:14:52 -04:00
settings/helpTemplates Replaced local drmaa and Jama artifacts with versions from maven central. 2014-02-22 01:21:35 +08:00
.gitignore Fixed bug using GraphBased due to infinite likelihoods resulting from the calculation of alignment cost of very long insertion or deletions (done in linear scale) 2014-04-01 16:14:52 -04:00
README.md Update README file for the 2.6 release 2013-06-20 13:08:29 -04:00
ant-bridge.sh Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests 2014-03-10 21:24:03 -04:00
intellij_example.tar.bz2 Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!) 2012-09-27 11:04:56 -04:00
pom.xml Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00

README.md

The Genome Analysis Toolkit

See http://www.broadinstitute.org/gatk/