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
..
engine	When running Queue jobs locally, merge the stderr to the stdout log if the error file is NOT specified.	2012-01-10 16:10:25 -05:00
extensions	Be explicit about setting the snpEff -onlyCoding option in the pipeline	2012-01-17 20:04:27 -05:00
function	General improvements to Queue	2011-12-20 14:05:09 -05:00
library	During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice.	2011-11-17 13:56:42 -05:00
util	Support for NT testing (default up to 4) for CC and UG	2011-12-14 18:45:00 -05:00
QCommandLine.scala	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
QException.scala	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
QScript.scala	Now captures the exechost in the job report	2011-08-28 12:05:56 -04:00
QScriptManager.scala	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
QSettings.scala	General improvements to Queue	2011-12-20 14:05:09 -05:00