Guillermo del Angel 827be878b4 Bug fix when running UG in GenotypeGivenAlleles mode: if an input site to genotype had no coverage, the output VCF had AC,AF and AN inherited from input VCF, which could have nothing to do with given BAM so numbers could be non-sensical. Now new vc has clear attributes instead of attributes inherited from input VCF.		2012-02-06 11:58:13 -05:00
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R	Protect ourselves when iteration is present but there's only a single iteration in queueJobReport.R	2011-12-19 10:08:38 -05:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
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	Bug fix when running UG in GenotypeGivenAlleles mode: if an input site to genotype had no coverage, the output VCF had AC,AF and AN inherited from input VCF, which could have nothing to do with given BAM so numbers could be non-sensical. Now new vc has clear attributes instead of attributes inherited from input VCF.	2012-02-06 11:58:13 -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	Be explicit about setting the snpEff -onlyCoding option in the pipeline	2012-01-17 20:04:27 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00