Disabling the queue/pipeline package by default so that scala code can build. If it's not going to be fixed the package should be removed. If it is going to be fixed this patch to build.xml should be reverted.

Also added the old model of indel calling to the FCP.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5749 348d0f76-0448-11de-a6fe-93d51630548a

build.xml

@@ -298,6 +298,13 @@
             <src path="${queue-extensions.source.dir}" />
             <include name="**/*.scala"/>
             <exclude name="**/gridengine/**" unless="include.gridengine" />
+            <!--
+            NOTE: Added include.queue.pipeline flag while VQSR v2 is being migrated
+            and the pipeline package is still using the old version.
+            At this moment enabling the flag turns on code that doesn't compile.
+            ASAP determine if package should use v2 or be retired.
+            -->
+            <exclude name="**/queue/pipeline/**" unless="include.queue.pipeline" />
         </scalac>
     </target>
 

scala/qscript/playground/FullCallingPipeline.q

@@ -94,6 +94,7 @@ class FullCallingPipeline extends QScript {
     indels.jobOutputFile = ".queue/logs/IndelCalling/UnifiedGenotyper.indels.out"
     indels.downsample_to_coverage = 600
     indels.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.INDEL
+    indels.GSA_PRODUCTION_ONLY = true /* use old indel genotyper */
     indels.input_file = List(writeBamList.listFile)
     indels.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
     indels.out = "IndelCalls/" + base+".indels.vcf"