Mark DePristo f8a0a947e3 Critical bugfix for GSA-652 / Multi-threaded VCF -> BCF writing produces invalid intermediate file that fails on merging ... -- New tribble library now uses 64 bit sizes. The 26K VCF has so much data that low-level tribble block indices where overflowing their int size values. This includes a to-be-committed tribble jar that fixes this problem -- See https://jira.broadinstitute.org/browse/GSA-652 -- Minor cleanup of error messages that were useful on the way to solving this monster problem		2012-11-02 09:09:59 -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	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Critical bugfix for GSA-652 / Multi-threaded VCF -> BCF writing produces invalid intermediate file that fails on merging	2012-11-02 09:09:59 -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	Only run UG in the bundle for chr20	2012-10-30 15:09:46 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00