Mauricio Carneiro 2bb9525e7f Don't set base qualities if fastQ is provided ... * Pacbio Processing pipeline now works with the new fastQ files outputted by the Pacbio instrument		2012-01-23 17:57:29 -05:00
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examples	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
lib	moving the example scala scripts to the qscripts package.	2011-07-01 16:14:59 -04:00
DataProcessingPipeline.scala	No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice.	2012-01-08 12:11:55 -05:00
GATKResourcesBundle.scala	Replacing Mills file with new gold standard indel set in the resource bundle for release with v1.5	2012-01-17 15:02:45 -05:00
MethodsDevelopmentCallingPipeline.scala	adding dbsnp to indel VQSR	2012-01-10 12:38:49 -05:00
PacbioProcessingPipeline.scala	Don't set base qualities if fastQ is provided	2012-01-23 17:57:29 -05:00