From d047c19ad1a6a5087425a0321340aa24adf7b82f Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 24 Aug 2011 13:52:05 -0400
Subject: [PATCH] Writes output to file

---
 .../org/broadinstitute/sting/queue/QCommandLine.scala    | 4 +++-
 .../org/broadinstitute/sting/queue/util/JobLogging.scala | 9 +++++----
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
index becd1e1cf..c6d1f3883 100755
--- a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
@@ -115,7 +115,9 @@ class QCommandLine extends CommandLineProgram with Logging {
     // walk over each script, calling onExecutionDone
     for (script <- allQScripts) {
       script.onExecutionDone(qGraph.getFunctionsAndStatus(script.functions), qGraph.success)
-      JobLogging.printLogs(qGraph.getFunctionsAndStatus(script.functions))
+      val reportFile = new File("joblogging.gatkreport.txt")
+      logger.info("Writing JobLogging GATKReport to file " + reportFile)
+      JobLogging.printLogs(qGraph.getFunctionsAndStatus(script.functions), reportFile)
     }
 
     if (!qGraph.success) {
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/JobLogging.scala b/public/scala/src/org/broadinstitute/sting/queue/util/JobLogging.scala
index d24ebe92b..3bb43508a 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/JobLogging.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/JobLogging.scala
@@ -27,6 +27,7 @@ import org.broadinstitute.sting.queue.function.QFunction
 import org.broadinstitute.sting.gatk.report.{GATKReportTable, GATKReport}
 import org.broadinstitute.sting.utils.exceptions.UserException
 import org.broadinstitute.sting.queue.engine.JobRunInfo
+import java.io.{FileOutputStream, PrintStream, File}
 
 /**
  * A mixin to add Job info to the class
@@ -70,10 +71,10 @@ trait JobLogging extends QFunction {
 }
 
 object JobLogging {
-  def printLogs(jobs: Map[QFunction, JobRunInfo]) {
+  def printLogs(jobs: Map[QFunction, JobRunInfo], dest: File) {
     val jobLogs: List[JobLogging] = jobLoggingSublist(jobs.keys.toList)
     jobLogs.foreach((job: JobLogging) => job.addRunInfo(jobs.get(job).get))
-    printJobLogging(jobLogs)
+    printJobLogging(jobLogs, new PrintStream(new FileOutputStream(dest)))
   }
 
   private def jobLoggingSublist(l: List[QFunction]): List[JobLogging] = {
@@ -89,7 +90,7 @@ object JobLogging {
    * Prints the JobLogging logs to a GATKReport.  First splits up the
    * logs by group, and for each group generates a GATKReportTable
    */
-  private def printJobLogging(logs: List[JobLogging]) {
+  private def printJobLogging(logs: List[JobLogging], stream: PrintStream) {
     // create the report
     val report: GATKReport = new GATKReport
 
@@ -108,7 +109,7 @@ object JobLogging {
       }
     }
 
-    report.print(System.out)
+    report.print(stream)
   }
 
   private def groupLogs(logs: List[JobLogging]): Map[String, List[JobLogging]] = {