Mark DePristo f2b0575dee Detect unreasonably large allele strings (>2^16) and throw an error ... -- samtools can emit alleles where the ref is 42M Ns and this caused the GATK (via tribble) to hang in several places. -- Tribble was updated so we actually could read the line properly (rev. to 51 here). -- Still the parsing algorithms in the GATK aren't happy with such a long allele. Instead of optimizing the code around an improper use case I put in a limit of 2^16 bp for any allele, and throw a meaningful exception when encountered.		2012-01-17 16:40:26 -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	Detect unreasonably large allele strings (>2^16) and throw an error	2012-01-17 16:40:26 -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