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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
..
VectorPairHMM Removed g_haplotype* global variables in native code so that it works 2014-03-06 22:08:35 -08:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles
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doc Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
external-example Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
gatk-framework 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
gatk-package Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
gatk-queue-extgen Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
gsalib Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
java/config Moved files to maven directories. 2014-02-03 13:50:44 -05:00
package-tests Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
queue-framework Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
queue-package Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
repo Rev Picard 1.110.1773 2014-03-31 14:15:06 -04:00
sting-root Rev Picard 1.110.1773 2014-03-31 14:15:06 -04:00
sting-utils Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
pom.xml Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00