David Roazen d5199db8ec Be explicit about setting the snpEff -onlyCoding option in the pipeline ... When run without an explicit -onlyCoding option, as we've been doing up to now, snpEff automatically sets -onlyCoding to "true" provided that there is at least one transcript marked as "protein_coding", which will always be the case for us in practice (and indeed, all pipeline runs so far with snpEff 2.0.5 have run with -onlyCoding auto-set to "true"). However, given the disastrous effect on annotation quality setting "-onlyCoding false" has, we wish to be explicit with this option rather than relying on snpEff's auto-detection logic.		2012-01-17 20:04:27 -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	Error message cleanup in BAM indexing code.	2012-01-17 11:05:42 -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