Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

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

@@ -10,13 +10,17 @@ class ExampleRetryMemoryLimit extends QScript {
   var bamFile: File = _
 
   def script() {
-    val ug = new UnifiedGenotyper with RetryMemoryLimit
+    for (scatterCount <- 1 to 2) {
-    // First run with 1m
+      val ug = new UnifiedGenotyper with RetryMemoryLimit
-    ug.memoryLimit = .001
+      // First run with 1m
-    // On retry run with 1g
+      ug.memoryLimit = .001
-    ug.retryMemoryFunction = (d => d * 1000)
+      // On retry run with 1g
-    ug.reference_sequence = referenceFile
+      ug.retryMemoryFunction = (d => d * 1000)
-    ug.input_file = Seq(bamFile)
+      ug.reference_sequence = referenceFile
-    add(ug)
+      ug.input_file = Seq(bamFile)
+      ug.out = swapExt(bamFile, ".bam", ".scattered_%d.vcf".format(scatterCount))
+      ug.scatterCount = scatterCount
+      add(ug)
+    }
   }
 }

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala

@@ -26,19 +26,19 @@ package org.broadinstitute.sting.queue.extensions.gatk
 
 import org.broadinstitute.sting.queue.function.scattergather.GatherFunction
 import org.broadinstitute.sting.queue.extensions.picard.PicardBamFunction
-import org.broadinstitute.sting.queue.function.QFunction
+import org.broadinstitute.sting.queue.function.{RetryMemoryLimit, QFunction}
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor
 
 /**
  * Merges BAM files using net.sf.picard.sam.MergeSamFiles.
  */
-class BamGatherFunction extends GatherFunction with PicardBamFunction {
+class BamGatherFunction extends GatherFunction with PicardBamFunction with RetryMemoryLimit {
   this.javaMainClass = "net.sf.picard.sam.MergeSamFiles"
   this.assumeSorted = Some(true)
   protected def inputBams = gatherParts
   protected def outputBam = originalOutput
 
-  override def freezeFieldValues {
+  override def freezeFieldValues() {
     val originalGATK = originalFunction.asInstanceOf[CommandLineGATK]
 
     // Whatever the original function can handle, merging *should* do less.

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala

@@ -25,13 +25,13 @@
 package org.broadinstitute.sting.queue.extensions.gatk
 
 import org.broadinstitute.sting.queue.function.scattergather.GatherFunction
-import org.broadinstitute.sting.queue.function.QFunction
+import org.broadinstitute.sting.queue.function.{RetryMemoryLimit, QFunction}
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor
 
 /**
  * Merges a vcf text file.
  */
-class VcfGatherFunction extends CombineVariants with GatherFunction {
+class VcfGatherFunction extends CombineVariants with GatherFunction with RetryMemoryLimit {
   this.assumeIdenticalSamples = true
   this.suppressCommandLineHeader = true
 

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala

@@ -50,7 +50,7 @@ class SortSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFun
   override def freezeFieldValues() {
     super.freezeFieldValues()
     if (outputIndex == null && output != null)
-      outputIndex = new File(output.getName.stripSuffix(".bam") + ".bai")
+      outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
   }
 
 

public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala

@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.queue.function
 
 import org.broadinstitute.sting.queue.util._
+import org.broadinstitute.sting.commandline.Argument
 
 /**
  * A command line that will be run in a pipeline.
@@ -33,12 +34,15 @@ trait CommandLineFunction extends QFunction with Logging {
   def commandLine: String
 
   /** Upper memory limit */
+  @Argument(doc="Memory limit", required=false)
   var memoryLimit: Option[Double] = None
 
   /** Resident memory limit */
+  @Argument(doc="Resident memory limit", required=false)
   var residentLimit: Option[Double] = None
 
   /** Resident memory request */
+  @Argument(doc="Resident memory request", required=false)
   var residentRequest: Option[Double] = None
 
   /** the number of SMP cores this job wants */

public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala

@@ -47,6 +47,7 @@ trait JavaCommandLineFunction extends CommandLineFunction {
   /**
    * Memory limit for the java executable, or if None will use the default memoryLimit.
    */
+  @Argument(doc="Java memory limit", required=false)
   var javaMemoryLimit: Option[Double] = None
 
   /**

public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala

@@ -113,11 +113,13 @@ trait QFunction extends Logging with QJobReport {
   var jobErrorFile: File = _
 
   /** Errors (if any) from the last failed run of jobErrorFiles. */
+  @Argument(doc="Job error lines", required=false)
   var jobErrorLines: Seq[String] = Nil
 
   /**
    * The number of times this function has previously been run.
    */
+  @Argument(doc="Job retries", required=false)
   var retries = 0
 
   /** Change settings for the next run. Retries will be set to the number of times the function was run and jobErrorLines may contain the error text. */
@@ -541,4 +543,11 @@ object QFunction {
         classFields
     }
   }
+
+  /**
+   * Returns the Seq of fields for a QFunction class.
+   * @param clazz Class to retrieve fields for.
+   * @return the fields of the class.
+   */
+  def classFunctionFields(clazz: Class[_]) = classFields(clazz).functionFields
 }

public/scala/src/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala

@@ -24,17 +24,26 @@
 
 package org.broadinstitute.sting.queue.function
 
+import org.broadinstitute.sting.commandline.Argument
+
+object RetryMemoryLimit {
+  private val defaultRetryMemoryFunction: (Double => Double) = ( 2 * _ )
+  private val defaultMemoryLimitErrorText = Seq("OutOfMemory", "you did not provide enough memory", "TERM_MEMLIMIT")
+}
+
 /** A mixin that on retry increases the memory limit when certain text is found. */
 trait RetryMemoryLimit extends CommandLineFunction {
 
   /** How to increase the memory. By default doubles the memory. */
-  var retryMemoryFunction: (Double => Double) = (2 * _)
+  var retryMemoryFunction: (Double => Double) = RetryMemoryLimit.defaultRetryMemoryFunction
 
   /** Once the threshold is passed, no more memory will be added to memory limit. */
+  @Argument(doc="threshold to stop doubling the memory", required=false)
   var memoryLimitThreshold: Option[Double] = None
 
   /** Various strings to look for to determine we ran out of memory. */
-  var memoryLimitErrorText = Seq("OutOfMemory", "you did not provide enough memory", "TERM_MEMLIMIT")
+  @Argument(doc="text to look for in the errors", required = false)
+  var memoryLimitErrorText = RetryMemoryLimit.defaultMemoryLimitErrorText
 
   override def freezeFieldValues() {
     super.freezeFieldValues()
@@ -42,6 +51,21 @@ trait RetryMemoryLimit extends CommandLineFunction {
       this.memoryLimitThreshold = this.qSettings.memoryLimitThreshold
   }
 
+
+  override def copySettingsTo(function: QFunction) {
+    super.copySettingsTo(function)
+    function match {
+      case retryMemoryLimit: RetryMemoryLimit =>
+        if (retryMemoryLimit.memoryLimitThreshold.isEmpty)
+          retryMemoryLimit.memoryLimitThreshold = this.memoryLimitThreshold
+        if (retryMemoryLimit.retryMemoryFunction == RetryMemoryLimit.defaultRetryMemoryFunction)
+          retryMemoryLimit.retryMemoryFunction = this.retryMemoryFunction
+        if (retryMemoryLimit.memoryLimitErrorText == RetryMemoryLimit.defaultMemoryLimitErrorText)
+          retryMemoryLimit.memoryLimitErrorText = this.memoryLimitErrorText
+      case _ => /* ignore */
+    }
+  }
+
   override def setupRetry() {
     super.setupRetry()
     if (this.memoryLimitThreshold.isDefined && this.memoryLimit.isDefined) {

public/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala

@@ -30,6 +30,10 @@ import org.broadinstitute.sting.queue.function.{QFunction, CommandLineFunction}
 /**
  * Shadow clones another command line function.
  */
+object CloneFunction {
+  private lazy val cloneFunctionFields = QFunction.classFunctionFields(classOf[CloneFunction])
+}
+
 class CloneFunction extends CommandLineFunction {
   var originalFunction: ScatterGatherableFunction = _
   var cloneIndex: Int = _
@@ -41,10 +45,10 @@ class CloneFunction extends CommandLineFunction {
     var originalValues = Map.empty[ArgumentSource, Any]
     withScatterPartCount += 1
     if (withScatterPartCount == 1) {
-      overriddenFields.foreach{
+      originalFunction.functionFields.foreach {
-        case (field, overrideValue) => {
+        case (field) => {
           originalValues += field -> originalFunction.getFieldValue(field)
-          originalFunction.setFieldValue(field, overrideValue)
+          originalFunction.setFieldValue(field, getFieldValue(field))
         }
       }
     }
@@ -52,9 +56,11 @@ class CloneFunction extends CommandLineFunction {
       f()
     } finally {
       if (withScatterPartCount == 1) {
-        originalValues.foreach{
+        originalFunction.functionFields.foreach {
-          case (name, value) =>
+          case (field) => {
-            originalFunction.setFieldValue(name, value)
+            setFieldValue(field, originalFunction.getFieldValue(field))
+            originalFunction.setFieldValue(field, originalValues(field))
+          }
         }
       }
       withScatterPartCount -= 1
@@ -63,6 +69,8 @@ class CloneFunction extends CommandLineFunction {
 
   override def description = withScatterPart(() => originalFunction.description)
   override def shortDescription = withScatterPart(() => originalFunction.shortDescription)
+  override def setupRetry() { withScatterPart(() => originalFunction.setupRetry()) }
+
   override protected def functionFieldClass = originalFunction.getClass
 
   def commandLine = withScatterPart(() => originalFunction.commandLine)
@@ -73,13 +81,19 @@ class CloneFunction extends CommandLineFunction {
   }
 
   override def getFieldValue(source: ArgumentSource): AnyRef = {
-    overriddenFields.get(source) match {
+    CloneFunction.cloneFunctionFields.find(_.field.getName == source.field.getName) match {
-      case Some(value) => value.asInstanceOf[AnyRef]
+      case Some(cloneSource) =>
-      case None => {
+        super.getFieldValue(cloneSource)
-        val value = originalFunction.getFieldValue(source)
+      case None =>
-        overriddenFields += source -> value
+        overriddenFields.get(source) match {
-        value
+          case Some(value) =>
-      }
+            value.asInstanceOf[AnyRef]
+          case None => {
+            val value = originalFunction.getFieldValue(source)
+            overriddenFields += source -> value
+            value
+          }
+        }
     }
   }