Mark DePristo 763c81d520 No longer enforce MAX_ALLELE_SIZE in VCF codec ... -- Instead issue a warning when a large (>1MB) record is encountered -- Optimized ref.getBytes()[i] => (byte)ref.charAt(i), which avoids an implicit O(n) allocation each iteration through computeReverseClipping()		2012-01-18 07:35:11 -05:00
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R	queueJobReport now compresses PDF when running R 2.13+.	2012-01-10 17:32:30 -05:00
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	No longer enforce MAX_ALLELE_SIZE in VCF codec	2012-01-18 07:35:11 -05:00
packages	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Replacing Mills file with new gold standard indel set in the resource bundle for release with v1.5	2012-01-17 15:02:45 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00