Ryan Poplin 1bdf17ef53 Reworking of how the likelihood calculation is organized in the HaplotypeCaller to facilitate the inclusion of per allele downsampling. We now use the downsampling for both the GL calculations and the annotation calculations.		2012-12-02 11:58:32 -05:00
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R	Fix a nasty bug in reading GATK reports with a single line	2012-09-10 20:14:13 -04:00
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java	Reworking of how the likelihood calculation is organized in the HaplotypeCaller to facilitate the inclusion of per allele downsampling. We now use the downsampling for both the GL calculations and the annotation calculations.	2012-12-02 11:58:32 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Fixed fragment handling in DepthOfCoverage	2012-11-21 16:01:10 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00