Bringing in the changes from the CMI repo

protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java

@@ -17,6 +17,7 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
     final String COREDUCTION_BAM_A = validationDataLocation + "coreduction.test.A.bam";
     final String COREDUCTION_BAM_B = validationDataLocation + "coreduction.test.B.bam";
     final String COREDUCTION_L = " -L 1:1,853,860-1,854,354 -L 1:1,884,131-1,892,057";
+    final String OFFCONTIG_BAM = privateTestDir + "readOffb37contigMT.bam";
 
     private void RRTest(String testName, String args, String md5) {
         String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, BAM) + " -o %s ";
@@ -86,5 +87,15 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
         executeTest("testCoReduction", new WalkerTestSpec(base, Arrays.asList("5c30fde961a1357bf72c15144c01981b")));
     }
 
+    /**
+     * Bug happens when reads are soft-clipped off the  contig (usually in the MT). This test guarantees no changes to the upstream code will
+     * break the current hard-clipping routine that protects reduce reads from such reads.
+     */
+    @Test(enabled = true)
+    public void testReadOffContig() {
+        String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, OFFCONTIG_BAM) + " -o %s ";
+        executeTest("testReadOffContig", new WalkerTestSpec(base, Arrays.asList("53e16367d333da0b7d40a7683a35c95f")));
+    }
+
 }
 

public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java

@@ -397,9 +397,6 @@ public class GATKSAMRecord extends BAMRecord {
                 else if (op != CigarOperator.HARD_CLIP)
                     break;
             }
-
-            if ( softStart < 1 )
-                softStart = 1;
         }
         return softStart;
     }

public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala

@@ -110,6 +110,9 @@ class QCommandLine extends CommandLineProgram with Logging {
    * functions, and then builds and runs a QGraph based on the dependencies.
    */
   def execute = {
+    var success = false
+    var result = 1
+    try {
       ClassFieldCache.parsingEngine = this.parser
 
       if (settings.qSettings.runName == null)
@@ -166,7 +169,6 @@ class QCommandLine extends CommandLineProgram with Logging {
       qGraph.run()
 
       val functionsAndStatus = qGraph.getFunctionsAndStatus
-    val success = qGraph.success
 
       // walk over each script, calling onExecutionDone
       for (script <- allQScripts) {
@@ -180,14 +182,7 @@ class QCommandLine extends CommandLineProgram with Logging {
       logger.info("Writing final jobs report...")
       qGraph.writeJobsReport()
 
-    if (!success) {
+      if (qGraph.success) {
-      logger.info("Done with errors")
-      qGraph.logFailed()
-      for (commandPlugin <- allCommandPlugins)
-        if (commandPlugin.statusMessenger != null)
-          commandPlugin.statusMessenger.exit("Done with errors: %s".format(qGraph.formattedStatusCounts))
-      1
-    } else {
         if (settings.run) {
           allQScripts.foreach(_.pushOutputs())
           for (commandPlugin <- allCommandPlugins)
@@ -197,8 +192,21 @@ class QCommandLine extends CommandLineProgram with Logging {
               commandPlugin.statusMessenger.done(allInputs, allOutputs)
             }
         }
-      0
+        success = true
+        result = 0
       }
+    } finally {
+      if (!success) {
+        logger.info("Done with errors")
+        qGraph.logFailed()
+        if (settings.run) {
+          for (commandPlugin <- allCommandPlugins)
+            if (commandPlugin.statusMessenger != null)
+              commandPlugin.statusMessenger.exit("Done with errors: %s".format(qGraph.formattedStatusCounts))
+        }
+      }
+    }
+    result
   }
 
   /**

public/scala/src/org/broadinstitute/sting/queue/QScript.scala

@@ -124,7 +124,7 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon
   }
 
   /**
-   * Pull all remote files to the local disk.
+   * Pull all remote files to the local disk
    */
   def pullInputs() {
     val inputs = ClassFieldCache.getFieldFiles(this, inputFields)
@@ -135,7 +135,7 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon
   }
 
   /**
-   * Push all remote files from the local disk.
+   * Push all remote files from the local disk
    */
   def pushOutputs() {
     val outputs = ClassFieldCache.getFieldFiles(this, outputFields)
@@ -145,28 +145,17 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon
     }
   }
 
-  /**
-   * List out the remote outputs
-   * @return the RemoteFile outputs by argument source
-   */
-  def remoteInputs: Map[String, Seq[RemoteFile]] = tagMap(remoteFieldMap(inputFields))
-
-  /**
-   * List out the remote outputs
-   * @return the RemoteFile outputs by argument source
-   */
-  def remoteOutputs: Map[String, Seq[RemoteFile]] = tagMap(remoteFieldMap(outputFields))
-
-  private def tagMap(remoteFieldMap: Map[ArgumentSource, Seq[RemoteFile]]): Map[String, Seq[RemoteFile]] = {
-    remoteFieldMap.collect{ case (k, v) => ClassFieldCache.fullName(k) -> v }.toMap
-  }
-
-  private def remoteFieldMap(fields: Seq[ArgumentSource]): Map[ArgumentSource, Seq[RemoteFile]] = {
-    fields.map(field => (field -> filterRemoteFiles(ClassFieldCache.getFieldFiles(this, field)))).filter(tuple => !tuple._2.isEmpty).toMap
-  }
-
   private def filterRemoteFiles(fields: Seq[File]): Seq[RemoteFile] =
     fields.filter(field => field != null && field.isInstanceOf[RemoteFile]).map(_.asInstanceOf[RemoteFile])
+  /**
+   * @return the inputs or null if there are no inputs
+   */
+  def remoteInputs: AnyRef = null
+
+  /**
+   * @return the outputs or null if there are no outputs
+   */
+  def remoteOutputs: AnyRef = null
 
   /** The complete list of fields. */
   def functionFields: Seq[ArgumentSource] = ClassFieldCache.classFunctionFields(this.getClass)

public/scala/src/org/broadinstitute/sting/queue/engine/QStatusMessenger.scala

@@ -7,7 +7,7 @@ import org.broadinstitute.sting.queue.util.RemoteFile
  */
 trait QStatusMessenger {
   def started()
-  def done(inputs: Seq[Map[String, Seq[RemoteFile]]], outputs: Seq[Map[String, Seq[RemoteFile]]])
+  def done(inputs: Seq[_], outputs: Seq[_])
   def exit(message: String)
 
   def started(job: String)