From 851e1df0728877791e656bcfbae93506c5a97f70 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 2 Mar 2009 21:51:25 +0000
Subject: [PATCH] reconciled TraversalEngine

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@21 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/build.xml                                |  5 +++--
 .../mit/broad/sting/atk/TraversalEngine.java  | 22 ++++++++++---------
 scripts/TraverseTest.sh                       |  2 +-
 scripts/TraverseTestProf.sh                   |  2 +-
 4 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/java/build.xml b/java/build.xml
index 38496e0f6..d3b95aecf 100644
--- a/java/build.xml
+++ b/java/build.xml
@@ -6,7 +6,8 @@
   <property name="src" location="trunk/java/"/>
   <property name="build" location="out/production/AnalysisTK"/>
   <property name="dist"  location="dist"/>
-
+  <property name="jars"  location="trunk/java/jars/functionalj.jar"/>
+  
   <target name="init">
     <!-- Create the time stamp -->
     <tstamp/>
@@ -17,7 +18,7 @@
   <target name="compile" depends="init"
         description="compile the source " >
     <!-- Compile the java code from ${src} into ${build} -->
-    <javac srcdir="${src}" destdir="${build}"/>
+    <javac srcdir="${src}" destdir="${build}" classpath="${jars}"/>
   </target>
 
   <target name="dist" depends="compile"
diff --git a/java/src/edu/mit/broad/sting/atk/TraversalEngine.java b/java/src/edu/mit/broad/sting/atk/TraversalEngine.java
index f58aee30f..a6399bcf6 100755
--- a/java/src/edu/mit/broad/sting/atk/TraversalEngine.java
+++ b/java/src/edu/mit/broad/sting/atk/TraversalEngine.java
@@ -146,17 +146,18 @@ public class TraversalEngine {
     // functions for dealing with the reference sequence
     //
     // --------------------------------------------------------------------------------------------------------------
-    public void printProgress(final String type) { printProgress( false, type ); }
+    public void printProgress(final String type, GenomeLoc loc) { printProgress( false, type, loc ); }
 
-    public void printProgress( boolean mustPrint, final String type ) {
+    public void printProgress( boolean mustPrint, final String type, GenomeLoc loc ) {
         final long nRecords = this.nRecords;
 
         if ( mustPrint || nRecords % 100000 == 0 ) {
             final double elapsed = (System.currentTimeMillis() - startTime) / 1000.0;
             final double secsPer1MReads = (elapsed * 1000000.0) / nRecords;
-
-            System.out.printf("Traversed %d %s %.2f secs (%.2f secs per 1M %s)%n", nRecords, type, elapsed, secsPer1MReads, type);
-            
+            if ( loc != null )
+                System.out.printf("Traversed to %s, processing %d %s %.2f secs (%.2f secs per 1M %s)%n", loc, nRecords, type, elapsed, secsPer1MReads, type);
+            else
+                System.out.printf("Traversed %d %s %.2f secs (%.2f secs per 1M %s)%n", nRecords, type, elapsed, secsPer1MReads, type);
             System.out.printf("  -> %s%n", samReadingTracker.progressMeter());
         }
     }
@@ -297,14 +298,15 @@ public class TraversalEngine {
                     done = true;
                 }
 
-                printProgress("loci");
+
             }
 
+            printProgress("loci", locus.getLocation());
             if ( pastFinalLocation(locus.getLocation()) )
                 done = true;
         }
 
-        printProgress( true, "loci" );
+        printProgress( true, "loci", null );
         System.out.println("Traversal reduce result is " + sum);
         System.out.printf("Traversal skipped %d reads out of %d total (%.2f%%)%n", nSkippedReads, nReads, (nSkippedReads * 100.0) / nReads);
         System.out.printf("  -> %d unmapped reads%n", nUnmappedReads );
@@ -345,7 +347,7 @@ public class TraversalEngine {
                     break;
                 }
 
-                printProgress("reads");
+                printProgress("reads", loc);
             }
             
             if ( pastFinalLocation(loc) )
@@ -353,9 +355,9 @@ public class TraversalEngine {
             //System.out.printf("Done? %b%n", done);
          }
 
-        printProgress( true, "reads" );
+        printProgress( true, "reads", null );
         System.out.println("Traversal reduce result is " + sum);
         walker.onTraveralDone();
         return 0;
     }
-}
\ No newline at end of file
+}
diff --git a/scripts/TraverseTest.sh b/scripts/TraverseTest.sh
index d39c05437..b83cf95b4 100755
--- a/scripts/TraverseTest.sh
+++ b/scripts/TraverseTest.sh
@@ -1 +1 @@
-java -Xmx1024m -cp out/production/AnalysisTK:trunk/java/jars/functionalj.jar edu.mit.broad.sting.atk.AnalysisTK $*
+java -Xmx4096m -cp out/production/AnalysisTK:trunk/java/jars/functionalj.jar edu.mit.broad.sting.atk.AnalysisTK $*
diff --git a/scripts/TraverseTestProf.sh b/scripts/TraverseTestProf.sh
index c542c8337..18983a259 100755
--- a/scripts/TraverseTestProf.sh
+++ b/scripts/TraverseTestProf.sh
@@ -1 +1 @@
-java -Xmx1024m -agentlib:hprof=cpu=samples -cp out/production/AnalysisTK:trunk/java/jars/functionalj.jar edu.mit.broad.sting.atk.AnalysisTK $*
+java -Xmx4096m -agentlib:hprof=cpu=samples -cp out/production/AnalysisTK:trunk/java/jars/functionalj.jar edu.mit.broad.sting.atk.AnalysisTK $*