redo QC picard parts

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

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.queue.extensions.picard
 
 import org.broadinstitute.sting.commandline.{Argument, Output, Input}
 import java.io.File
+import net.sf.picard.analysis.MetricAccumulationLevel
 
 /**
  * Created with IntelliJ IDEA.
@@ -10,9 +11,9 @@ import java.io.File
  * Time: 5:59 PM
  * To change this template use File | Settings | File Templates.
  */
-class CalculateHsMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction {
+class CalculateHsMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction {
   analysisName = "CalculateHsMetrics"
-  javaMainClass = "net.sf.picard.sam.CalculateHsMetrics"
+  javaMainClass = "net.sf.picard.analysis.directed.CalculateHsMetrics"
 
   @Input(doc="The input SAM or BAM files to analyze.  Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
   var input: Seq[File] = Nil
@@ -28,33 +29,15 @@ class CalculateHsMetrics extends org.broadinstitute.sting.queue.function.JavaCom
 
   @Argument(doc="Reference file", shortName = "reference", fullName = "reference", required = true)
   var reference: File = _
- /*
-  @Argument(doc = "Maximum number of file handles to keep open when spilling read ends to disk.  Set this number a little lower than the per-process maximum number of file that may be open.  This number can be found by executing the 'ulimit -n' command on a Unix system.", shortName = "max_file_handles", fullName ="max_file_handles_for_read_ends_maps", required=false)
-  var MAX_FILE_HANDLES_FOR_READ_ENDS_MAP: Int = -1;
 
-  @Argument(doc = "This number, plus the maximum RAM available to the JVM, determine the memory footprint used by some of the sorting collections.  If you are running out of memory, try reducing this number.", shortName = "sorting_ratio", fullName = "sorting_collection_size_ratio", required = false)
+  val level = MetricAccumulationLevel.SAMPLE
-  var SORTING_COLLECTION_SIZE_RATIO: Double = -1
-   */
-  override def freezeFieldValues() {
-    super.freezeFieldValues()
-//    if (outputIndex == null && output != null)
-  //    outputIndex = new File(output.getName.stripSuffix(".bam") + ".bai")
-  }
-
-  val level = "SAMPLE"
 
   override def inputBams = input
-  override def outputBam = output
+  override def outputFile = output
-  //this.sortOrder = null
-  //this.createIndex = Some(true)
   override def commandLine = super.commandLine +
     required("BAIT_INTERVALS=" + baits) +
     required("TARGET_INTERVALS=" + targets) +
     required("REFERENCE_SEQUENCE=" + reference) +
-    optional("METRIC_ACCUMULATION_LEVEL="+level)/*+
+    optional("METRIC_ACCUMULATION_LEVEL="+level)
-    conditional(REMOVE_DUPLICATES, "REMOVE_DUPLICATES=true") +
-    conditional(MAX_FILE_HANDLES_FOR_READ_ENDS_MAP > 0, "MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=" + MAX_FILE_HANDLES_FOR_READ_ENDS_MAP.toString) +
-    conditional(SORTING_COLLECTION_SIZE_RATIO > 0, "SORTING_COLLECTION_SIZE_RATIO=" + SORTING_COLLECTION_SIZE_RATIO.toString)    */
-
 
 }

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

@@ -10,9 +10,9 @@ import java.io.File
  * Time: 10:37 AM
  * To change this template use File | Settings | File Templates.
  */
-class CollectGcBiasMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction {
+class CollectGcBiasMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction {
   analysisName = "CalculateGcMetrics"
-  javaMainClass = "net.sf.picard.sam.CalculateGcMetrics"
+  javaMainClass = "net.sf.picard.analysis.GcBiasSummaryMetrics"
 
   @Input(doc="The input SAM or BAM files to analyze.  Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
   var input: Seq[File] = Nil
@@ -24,7 +24,7 @@ class CollectGcBiasMetrics extends org.broadinstitute.sting.queue.function.JavaC
   var reference: File = _
 
   override def inputBams = input
-  override def outputBam = output
+  override def outputFile = output
   override def commandLine = super.commandLine +
     required("CHART_OUTPUT=" + output+".pdf") +
     required("REFERENCE_SEQUENCE=" + reference) +

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

@@ -10,9 +10,9 @@ import java.io.File
  * Time: 10:37 AM
  * To change this template use File | Settings | File Templates.
  */
-class CollectMultipleMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction{
+class CollectMultipleMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction{
   analysisName = "CalculateMultipleMetrics"
-  javaMainClass = "net.sf.picard.sam.CalculateMultipleMetrics"
+  javaMainClass = "net.sf.picard.analysis.CalculateMultipleMetrics"
 
   @Input(doc="The input SAM or BAM files to analyze.  Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
   var input: Seq[File] = Nil
@@ -24,7 +24,7 @@ class CollectMultipleMetrics extends org.broadinstitute.sting.queue.function.Jav
   var reference: File = _
 
   override def inputBams = input
-  override def outputBam = output
+  override def outputFile = output
   override def commandLine = super.commandLine +
     required("REFERENCE_SEQUENCE=" + reference) +
     required("ASSUME_SORTED=true") +