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 @@
GanttGroupShading
GanttVisibleRect
- {{-35, 39}, {1025, 1033}}
+ {{-35, 124}, {1025, 1033}}
OutlineVisibleRect
- {{0, 39}, {789, 1033}}
+ {{0, 124}, {789, 1033}}
ScaleWidths
Automatic
@@ -86,7 +86,7 @@
calendarController
OutlineVisibleRect
- {{0, 0}, {474, 720}}
+ {{0, 0}, {571, 830}}
activeColumnIdentifiers
IM
@@ -103,13 +103,13 @@
Notes
20
Resource
- 339
+ 436
Type
48
calendarSplit
- 0.67955440282821655
+ 0.67960631847381592
columnWidths
Effort
@@ -124,13 +124,13 @@
dayWidth
54
resourceSplit
- 0.56749671697616577
+ 0.56752324104309082
resourcesController
DayWidth
25
OutlineVisibleRect
- {{0, 0}, {645, 923}}
+ {{0, 0}, {776, 1033}}
ScaleWidths
Automatic
@@ -153,7 +153,7 @@
SelectedScale
Automatic
TimelineVisibleRect
- {{-1467, 0}, {823, 923}}
+ {{-1467, 0}, {995, 1033}}
activeColumnIdentifiers
IM
@@ -171,7 +171,7 @@
Notes
20
Resource
- 460
+ 591
Type
64
@@ -587,7 +587,7 @@
taskDifferenceEngine
nextId
- 109
+ 111
taskUserKeys
@@ -1230,6 +1230,7 @@
children
18
+ 109
19
37
33
@@ -2378,6 +2379,18 @@
workTime
8
+
+ effort
+ 28800
+ objectId
+ 109
+ task
+ Add mapping function from dict -> dict so we can process 1KG data against HS_18 assembly
+ workSeconds
+ 28800
+ workTime
+ 8
+
topResources
@@ -2388,7 +2401,7 @@
-1
uuid
- 7E48C9E3-9ADF-4CC6-BB69-412F6D01690A
+ E50852A9-C0BE-452A-A050-4FF83DEF06D7
version
2
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 -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