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Merge pull request #270 from broadinstitute/rp_reference_haplotype_mismatch_bug 

Fixing bug with dangling tails in which the tail connects all the way ba...
This commit is contained in:
Eric Banks 2013-06-12 11:03:48 -07:00
parent b2dc7095ab d1f397c711
commit 17d3ccb03b
3 changed files with 4 additions and 4 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
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@ -309,7 +309,7 @@ public class BaseGraph<V extends BaseVertex, E extends BaseEdge> extends Default
} }
v = getNextReferenceVertex(v); // advance along the reference path v = getNextReferenceVertex(v); // advance along the reference path
while( v != null && !v.equals(toVertex) ) { 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 v = getNextReferenceVertex(v); // advance along the reference path
} }
if( includeStop && v != null && v.equals(toVertex)) { 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); verticesToRemove.removeAll(onPathFromRefSource);
removeAllVertices(verticesToRemove); removeAllVertices(verticesToRemove);
// simple santity checks that this algorithm is working. // simple sanity checks that this algorithm is working.
if ( getSinks().size() > 1 ) { if ( getSinks().size() > 1 ) {
throw new IllegalStateException("Should have eliminated all but the reference sink, but found " + getSinks()); throw new IllegalStateException("Should have eliminated all but the reference sink, but found " + getSinks());
} }

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
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@ -207,7 +207,7 @@ public class ReadThreadingAssembler extends LocalAssemblyEngine {
* @return * @return
*/ */
private boolean reasonableNumberOfPaths(final SeqGraph graph) { 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); final List<Path<SeqVertex,BaseEdge>> allPaths = pathFinder.getKBestPaths(graph, 100000);
logger.info("Found " + allPaths.size() + " paths through " + graph + " with maximum " + maxAllowedPathsForReadThreadingAssembler); logger.info("Found " + allPaths.size() + " paths through " + graph + " with maximum " + maxAllowedPathsForReadThreadingAssembler);
return allPaths.size() <= maxAllowedPathsForReadThreadingAssembler; return allPaths.size() <= maxAllowedPathsForReadThreadingAssembler;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
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@ -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 // find the lowest common ancestor path between vertex and the reference sink if available
final List<MultiDeBruijnVertex> altPath = findPathToLowestCommonAncestorOfReference(vertex); final List<MultiDeBruijnVertex> altPath = findPathToLowestCommonAncestorOfReference(vertex);
if ( altPath == null ) if ( altPath == null || isRefSource(altPath.get(0)) )
return null; return null;
// now get the reference path from the LCA // now get the reference path from the LCA