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
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gatk-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
pom.xml	Update pom versions to mark the start of GATK 3.2 development	2014-03-18 01:18:59 -04:00