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Guillermo del Angel 5fac5bf12e Fixed issues with Queue packaging of Picard QC classes: separate jar's are needed fromPicard. User needs to specify the -picardBase argument to point to input path for jars. 
> Also, reenable joint cleaning as now it works.
> DEV-125 #resolve
> DEV-90 #resolve
 		2012-10-23 14:08:31 -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
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doc
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java Merge GATK repo into CMI-GATK 2012-10-23 10:59:11 -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 Fixed issues with Queue packaging of Picard QC classes: separate jar's are needed fromPicard. User needs to specify the -picardBase argument to point to input path for jars. 2012-10-23 14:08:31 -04:00
testdata Reverting move of BQSR tests to public, as per DR's email 2012-07-19 10:02:05 -04:00