Eric Banks 97b191f578 Thanks to Guillermo I was able to isolate an instance of where the MLEAC > AN. It turns out that this is valid, e.g. when PLs are all 0s for a sample we no-call it but it's allowed to factor into the MLE (since that's the contract with the exact model). Removing the check in UG and instead protecting for it in the AlleleCount stratification.		2012-08-20 01:16:23 -04:00
..
alignment	Killing off some FindBugs 'Realiability' issues	2012-08-16 14:00:48 -04:00
commandline	Fixed: GSA-392 @arguments with just a short name get the wrong argument bindings	2012-08-17 11:49:01 -04:00
gatk	Thanks to Guillermo I was able to isolate an instance of where the MLEAC > AN. It turns out that this is valid, e.g. when PLs are all 0s for a sample we no-call it but it's allowed to factor into the MLE (since that's the contract with the exact model). Removing the check in UG and instead protecting for it in the AlleleCount stratification.	2012-08-20 01:16:23 -04:00
jna	Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc.	2012-01-23 16:17:04 -05:00
queue	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
utils	Print "Parsing data stream with BCF version BCFx.y" in BCF2 codec as .debug not .info	2012-08-19 10:32:55 -04:00