a) Resolve [#DEV-56] - test data with indels in new directory private/testdata/CMITestData/. b) Skeleton (not yet working) of fastq-BAM unit test, c) misc bug fixes for QC functions to work (not done yet)

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

@@ -11,8 +11,8 @@ import java.io.File
  * To change this template use File | Settings | File Templates.
  */
 class CollectGcBiasMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction {
-  analysisName = "CalculateGcMetrics"
+  analysisName = "CollectGcBiasMetrics"
-  javaMainClass = "net.sf.picard.analysis.GcBiasSummaryMetrics"
+  javaMainClass = "net.sf.picard.analysis.CollectGcBiasMetrics"
 
   @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
@@ -26,6 +26,7 @@ class CollectGcBiasMetrics extends org.broadinstitute.sting.queue.function.JavaC
   override def inputBams = input
   override def outputFile = output
   override def commandLine = super.commandLine +
+    required("SUMMARY_OUTPUT=" + output) +
     required("CHART_OUTPUT=" + output+".pdf") +
     required("REFERENCE_SEQUENCE=" + reference) +
     required("ASSUME_SORTED=true")

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

@@ -11,8 +11,8 @@ import java.io.File
  * To change this template use File | Settings | File Templates.
  */
 class CollectMultipleMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction{
-  analysisName = "CalculateMultipleMetrics"
+  analysisName = "CollectMultipleMetrics"
-  javaMainClass = "net.sf.picard.analysis.CalculateMultipleMetrics"
+  javaMainClass = "net.sf.picard.analysis.CollectMultipleMetrics"
 
   @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

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

@@ -0,0 +1,53 @@
+/*
+ * Copyright (c) 2012, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.queue.extensions.picard
+
+import java.io.File
+import org.broadinstitute.sting.queue.function.JavaCommandLineFunction
+import net.sf.samtools.SAMFileReader.ValidationStringency
+import net.sf.samtools.SAMFileHeader.SortOrder
+
+/**
+ * Wraps a Picard function that operates on BAM files but doesn't output a new BAM file (i.e. QC metric files).
+ * See http://picard.sourceforge.net/ for more info.
+ *
+ * Since the various BAM utilities take slightly different arguments
+ * some values are optional.
+ */
+trait PicardMetricsFunction extends JavaCommandLineFunction {
+  var validationStringency = ValidationStringency.SILENT
+  var maxRecordsInRam: Option[Int] = None
+  var assumeSorted: Option[Boolean] = None
+  protected def inputBams: Seq[File]
+  protected def outputFile: File
+
+  abstract override def commandLine = super.commandLine +
+    repeat("INPUT=", inputBams, spaceSeparated=false) +
+    required("TMP_DIR=" + jobTempDir) +
+    optional("VALIDATION_STRINGENCY=", validationStringency, spaceSeparated=false) +
+    optional("OUTPUT=", outputFile, spaceSeparated=false) +
+    optional("MAX_RECORDS_IN_RAM=", maxRecordsInRam, spaceSeparated=false) +
+    optional("ASSUME_SORTED=", assumeSorted, spaceSeparated=false)
+}