Adding package information to scala scripts that were missing it. Including archived ones.

GSATDG-5

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala

@@ -1,23 +1,28 @@
-/*
+package org.broadinstitute.sting.queue.qscripts.examples
-* Copyright (c) 2012 The Broad Institute
+
-* 
+import org.broadinstitute.sting.queue.function.RetryMemoryLimit
-* Permission is hereby granted, free of charge, to any person
+import org.broadinstitute.sting.queue.QScript
-* obtaining a copy of this software and associated documentation
+import org.broadinstitute.sting.queue.extensions.gatk._
-* files (the "Software"), to deal in the Software without
+
-* restriction, including without limitation the rights to use,
+class ExampleRetryMemoryLimit extends QScript {
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
+  @Input(doc="The reference file for the bam files.", shortName="R")
-* copies of the Software, and to permit persons to whom the
+  var referenceFile: File = _
-* Software is furnished to do so, subject to the following
+
-* conditions:
+  @Input(doc="Bam file to genotype.", shortName="I")
-* 
+  var bamFile: File = _
-* The above copyright notice and this permission notice shall be
+
-* included in all copies or substantial portions of the Software.
+  def script() {
-* 
+    for (scatterCount <- 1 to 2) {
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+      val ug = new UnifiedGenotyper with RetryMemoryLimit
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+      // First run with 1m
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+      ug.memoryLimit = .001
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+      // On retry run with 1g
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+      ug.retryMemoryFunction = (d => d * 1000)
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+      ug.reference_sequence = referenceFile
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+      ug.input_file = Seq(bamFile)
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+      ug.out = swapExt(bamFile, ".bam", ".scattered_%d.vcf".format(scatterCount))
+      ug.scatterCount = scatterCount
+      add(ug)
+    }
+  }
+}