From 24e8581c30d8b1124f6bf45dd3dd1a26dac4b16d Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 2 Apr 2009 16:44:12 +0000
Subject: [PATCH] Slight improvements to allele caller interface; fixed problem
 with printing progress

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@260 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../contents.xml                              | 35 +++++++++++++------
 .../gatk/traversals/TraversalEngine.java      |  2 +-
 .../sting/gatk/traversals/TraverseByLoci.java |  1 +
 .../traversals/TraverseByLociByReference.java |  1 +
 .../gatk/walkers/AlleleFrequencyWalker.java   | 11 ++++--
 5 files changed, 35 insertions(+), 15 deletions(-)

diff --git a/doc/Genome Analysis TK plan.omniplan/contents.xml b/doc/Genome Analysis TK plan.omniplan/contents.xml
index 00ac6e2d0..c784b82f2 100644
--- a/doc/Genome Analysis TK plan.omniplan/contents.xml	
+++ b/doc/Genome Analysis TK plan.omniplan/contents.xml	
@@ -28,9 +28,9 @@
 			<key>GanttGroupShading</key>
 			<false/>
 			<key>GanttVisibleRect</key>
-			<string>{{-35, 39}, {1025, 1033}}</string>
+			<string>{{-35, 124}, {1025, 1033}}</string>
 			<key>OutlineVisibleRect</key>
-			<string>{{0, 39}, {789, 1033}}</string>
+			<string>{{0, 124}, {789, 1033}}</string>
 			<key>ScaleWidths</key>
 			<dict>
 				<key>Automatic</key>
@@ -86,7 +86,7 @@
 			<key>calendarController</key>
 			<dict>
 				<key>OutlineVisibleRect</key>
-				<string>{{0, 0}, {474, 720}}</string>
+				<string>{{0, 0}, {571, 830}}</string>
 				<key>activeColumnIdentifiers</key>
 				<array>
 					<string>IM</string>
@@ -103,13 +103,13 @@
 					<key>Notes</key>
 					<real>20</real>
 					<key>Resource</key>
-					<real>339</real>
+					<real>436</real>
 					<key>Type</key>
 					<real>48</real>
 				</dict>
 			</dict>
 			<key>calendarSplit</key>
-			<real>0.67955440282821655</real>
+			<real>0.67960631847381592</real>
 			<key>columnWidths</key>
 			<dict>
 				<key>Effort</key>
@@ -124,13 +124,13 @@
 			<key>dayWidth</key>
 			<real>54</real>
 			<key>resourceSplit</key>
-			<real>0.56749671697616577</real>
+			<real>0.56752324104309082</real>
 			<key>resourcesController</key>
 			<dict>
 				<key>DayWidth</key>
 				<real>25</real>
 				<key>OutlineVisibleRect</key>
-				<string>{{0, 0}, {645, 923}}</string>
+				<string>{{0, 0}, {776, 1033}}</string>
 				<key>ScaleWidths</key>
 				<dict>
 					<key>Automatic</key>
@@ -153,7 +153,7 @@
 				<key>SelectedScale</key>
 				<string>Automatic</string>
 				<key>TimelineVisibleRect</key>
-				<string>{{-1467, 0}, {823, 923}}</string>
+				<string>{{-1467, 0}, {995, 1033}}</string>
 				<key>activeColumnIdentifiers</key>
 				<array>
 					<string>IM</string>
@@ -171,7 +171,7 @@
 					<key>Notes</key>
 					<real>20</real>
 					<key>Resource</key>
-					<real>460</real>
+					<real>591</real>
 					<key>Type</key>
 					<real>64</real>
 				</dict>
@@ -587,7 +587,7 @@
 	<key>taskDifferenceEngine</key>
 	<dict>
 		<key>nextId</key>
-		<integer>109</integer>
+		<integer>111</integer>
 	</dict>
 	<key>taskUserKeys</key>
 	<array/>
@@ -1230,6 +1230,7 @@
 			<key>children</key>
 			<array>
 				<integer>18</integer>
+				<integer>109</integer>
 				<integer>19</integer>
 				<integer>37</integer>
 				<integer>33</integer>
@@ -2378,6 +2379,18 @@
 			<key>workTime</key>
 			<real>8</real>
 		</dict>
+		<dict>
+			<key>effort</key>
+			<real>28800</real>
+			<key>objectId</key>
+			<integer>109</integer>
+			<key>task</key>
+			<string>Add mapping function from dict -&gt; dict so we can process 1KG data against HS_18 assembly</string>
+			<key>workSeconds</key>
+			<real>28800</real>
+			<key>workTime</key>
+			<real>8</real>
+		</dict>
 	</array>
 	<key>topResources</key>
 	<array>
@@ -2388,7 +2401,7 @@
 		<integer>-1</integer>
 	</array>
 	<key>uuid</key>
-	<string>7E48C9E3-9ADF-4CC6-BB69-412F6D01690A</string>
+	<string>E50852A9-C0BE-452A-A050-4FF83DEF06D7</string>
 	<key>version</key>
 	<integer>2</integer>
 </dict>
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index da7b0ef84..cb0a15b7d 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
@@ -261,7 +261,7 @@ public abstract class TraversalEngine {
         final long nRecords = this.nRecords;
         final long curTime = System.currentTimeMillis();
         final double elapsed = (curTime - startTime) / 1000.0;
-        //System.out.printf("Cur = %d, last print = %d%n", curTime, lastProgressPrintTime);
+        //System.out.printf("Cur = %d, last print = %d, elapsed=%.2f, nRecords=%d, met=%b%n", curTime, lastProgressPrintTime, elapsed, nRecords, maxElapsedIntervalForPrinting(curTime));
 
         if (mustPrint || nRecords % N_RECORDS_TO_PRINT == 0 || maxElapsedIntervalForPrinting(curTime)) {
             this.lastProgressPrintTime = curTime;
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
index 33659b58c..821c254f6 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
@@ -131,6 +131,7 @@ public class TraverseByLoci extends TraversalEngine {
                     done = true;
                 }
 
+                printProgress("loci", locus.getLocation());
             }
 
             done = interval != null && locus.getLocation().isPast(interval);
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java
index 654d824a6..324398eb3 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java
@@ -86,6 +86,7 @@ public class TraverseByLociByReference extends TraverseByLoci {
                 done = true;
             }
             
+            printProgress("loci", locus.getLocation());
             refSite = refIter.next();                                       // update our location
         }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
index 2c07987e8..a02c3adff 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
@@ -399,8 +399,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
         tokens = alleleFreq.location.split(":");
         int current_offset = Integer.parseInt(tokens[1]);
 
-        if (inside_confident_ref_interval && 
-                ((alleleFreq.lodVsRef > -5.0) || (current_offset != last_position_considered + 1)))
+        if (inside_confident_ref_interval &&
+                ((alleleFreq.lodVsRef > -5.0) || (current_offset != last_position_considered + 1)) )
         {
             // No longer hom-ref, so output a ref line.
             tokens = confident_ref_interval_start.split(":");
@@ -469,7 +469,10 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
         try
         {
             this.random = new java.util.Random(0);
-            this.output = new PrintStream(GFF_OUTPUT_FILE);
+            if ( GFF_OUTPUT_FILE.equals("-") )
+                this.output = out;
+            else
+                this.output = new PrintStream(GFF_OUTPUT_FILE);
         }
         catch (Exception e)
         {
@@ -510,6 +513,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
         try
         {
 	        this.output.flush();
+            if ( ! GFF_OUTPUT_FILE.equals("-") )
+                this.output.close();
             this.output.close();
         }
         catch (Exception e)