Mark DePristo aeab932c63 Actual working version of unflushing VCFWriter ... -- Uses high-performance local writer backed by byte array that writes the entire VCF line in some write operation to the underlying output stream. -- Fixes problems with indexing of unflushed writes while still allowing efficient block zipping -- Same (or better) IO performance as previous implementation -- IndexingVariantContextWriter now properly closes the underlying output stream when it's closed -- Updated compressed VCF output file		2012-12-13 16:15:08 -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
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	Actual working version of unflushing VCFWriter	2012-12-13 16:15:08 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Update GATK packaging settings to package arbitrary resources	2012-11-28 15:26:05 -05:00
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	Add walltime changes to LSF	2012-11-29 15:23:37 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00