Mark DePristo cc8c12b954 Committing a broken version of BaseRecalibration ... -- I'm committing because there's some kind of fundamental problem with the ReadCovariates cache, in that historical data isn't being cleared / computed properly, and I'd rather it fail for a while than leave it in JIRA. -- The integration tests test the -nct with PrintReads to get 1, 2, 4 and the 4 fails. But that's because of this incorrect calculation -- Updating GATKPerformanceOverTime with the new @ClassType annotation		2012-10-25 14:46:35 -04:00
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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
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	…
doc	…
java	Committing a broken version of BaseRecalibration	2012-10-25 14:46:35 -04:00
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	Better error message when generic types are erased from scala collections.	2012-10-22 16:27:31 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00