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Mauricio Carneiro cd842b650e Optimizing DiagnoseTargets 
* Fixed output format to get a valid vcf
   * Optimzed the per sample pileup routine O(n^2) => O(n) pileup for samples
   * Added support to overlapping intervals
   * Removed expand target functionality (for now)
   * Removed total depth (pointless metric)
 		2012-04-10 17:43:59 -04:00
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R Further cleanup of R 2012-03-22 21:24:37 -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
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doc
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java Optimizing DiagnoseTargets 2012-04-10 17:43:59 -04:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
perl Update to the bindings for liftOverVCF.pl (to -V from -B) 2011-09-15 15:33:09 -04:00
scala Added more primitives to GATK Report Column Type 2012-03-28 09:07:54 -04:00
testdata continuing the BQSR triage... 2012-04-05 14:34:15 -04:00