From d1f397c7115e37dd4b54091a60b71fdb57260d89 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Wed, 12 Jun 2013 12:22:36 -0400
Subject: [PATCH] Fixing bug with dangling tails in which the tail connects all
 the way back to the reference source node.

-- List of vertices can't contain a source node.
---
 .../sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java  | 4 ++--
 .../haplotypecaller/readthreading/ReadThreadingAssembler.java | 2 +-
 .../haplotypecaller/readthreading/ReadThreadingGraph.java     | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
index 70ef539f3..2b37d90c2 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
@@ -309,7 +309,7 @@ public class BaseGraph<V extends BaseVertex, E extends BaseEdge> extends Default
         }
         v = getNextReferenceVertex(v); // advance along the reference path
         while( v != null && !v.equals(toVertex) ) {
-            bytes = ArrayUtils.addAll( bytes, getAdditionalSequence(v) );
+            bytes = ArrayUtils.addAll(bytes, getAdditionalSequence(v));
             v = getNextReferenceVertex(v); // advance along the reference path
         }
         if( includeStop && v != null && v.equals(toVertex)) {
@@ -561,7 +561,7 @@ public class BaseGraph<V extends BaseVertex, E extends BaseEdge> extends Default
         verticesToRemove.removeAll(onPathFromRefSource);
         removeAllVertices(verticesToRemove);
 
-        // simple santity checks that this algorithm is working.
+        // simple sanity checks that this algorithm is working.
         if ( getSinks().size() > 1 ) {
             throw new IllegalStateException("Should have eliminated all but the reference sink, but found " + getSinks());
         }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
index f4290f2bb..fc0f781c5 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
@@ -207,7 +207,7 @@ public class ReadThreadingAssembler extends LocalAssemblyEngine {
      * @return
      */
     private boolean reasonableNumberOfPaths(final SeqGraph graph) {
-        final KBestPaths<SeqVertex,BaseEdge> pathFinder = new KBestPaths<SeqVertex,BaseEdge>(false);
+        final KBestPaths<SeqVertex,BaseEdge> pathFinder = new KBestPaths<>(false);
         final List<Path<SeqVertex,BaseEdge>> allPaths = pathFinder.getKBestPaths(graph, 100000);
         logger.info("Found " + allPaths.size() + " paths through " + graph + " with maximum " + maxAllowedPathsForReadThreadingAssembler);
         return allPaths.size() <= maxAllowedPathsForReadThreadingAssembler;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
index 8d8cb83f6..0844f979b 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
@@ -339,7 +339,7 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
 
         // find the lowest common ancestor path between vertex and the reference sink if available
         final List<MultiDeBruijnVertex> altPath = findPathToLowestCommonAncestorOfReference(vertex);
-        if ( altPath == null )
+        if ( altPath == null || isRefSource(altPath.get(0)) )
             return null;
 
         // now get the reference path from the LCA