Updated version number.

Not populating simplification list when SIMPLIFY_AFTER_REMOVAL is false.
PapenfussLab · Feb 7, 2017 · 5279626 · 5279626
1 parent b32432b
commit 5279626
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Showing 3 changed files with 16 additions and 9 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 	<groupId>au.edu.wehi</groupId>
 	<artifactId>gridss</artifactId>
 	<packaging>jar</packaging>
-	<version>1.2.0</version>
+	<version>1.2.1</version>
 	<name>gridss</name>
 	<url>https://github.com/PapenfussLab/gridss</url>
 	<properties>

diff --git a/src/main/java/au/edu/wehi/idsv/debruijn/positional/NonReferenceContigAssembler.java b/src/main/java/au/edu/wehi/idsv/debruijn/positional/NonReferenceContigAssembler.java
@@ -33,7 +33,6 @@
 import au.edu.wehi.idsv.Defaults;
 import au.edu.wehi.idsv.DirectedEvidence;
 import au.edu.wehi.idsv.SanityCheckFailureException;
-import au.edu.wehi.idsv.configuration.AssemblyConfiguration;
 import au.edu.wehi.idsv.debruijn.DeBruijnGraphBase;
 import au.edu.wehi.idsv.debruijn.KmerEncodingHelper;
 import au.edu.wehi.idsv.graph.ScalingHelper;
@@ -177,7 +176,6 @@ private void ensureCalledContig() {
 		while (called.isEmpty()) {
 			// Safety calling to ensure loaded graph size is bounded
 			if (!nonReferenceGraphByPosition.isEmpty()) {
-				AssemblyConfiguration ap = aes.getContext().getAssemblyParameters();
 				int frontierStart = bestContigCaller.frontierStart(nextPosition());
 				// Need to make sure our contig that we're forcing a call on is comprised of evidence that has
 				// been fully loaded into the graph 
@@ -532,8 +530,13 @@ private void removeFromGraph(Set<KmerEvidence> evidence) {
 		if (bestContigCaller != null) {
 			bestContigCaller.remove(toRemove.keySet());
 		}
-		Set<KmerPathNode> simplifyCandidates = new ObjectOpenCustomHashSet<KmerPathNode>(new KmerPathNode.HashByFirstKmerStartPositionKmer<KmerPathNode>());
+		Set<KmerPathNode> simplifyCandidates = null;
+		if (SIMPLIFY_AFTER_REMOVAL) {
+			simplifyCandidates = new ObjectOpenCustomHashSet<KmerPathNode>(new KmerPathNode.HashByFirstKmerStartPositionKmer<KmerPathNode>());
+		}
 		for (Entry<KmerPathNode, List<List<KmerNode>>> entry : toRemove.entrySet()) {
+			// removing down-weighted replacement nodes from memoization is unnecessary since we just
+			// removed the entire node earlier in this function
 			removeWeight(entry.getKey(), entry.getValue(), simplifyCandidates, false);
 		}
 		if (SIMPLIFY_AFTER_REMOVAL) {
@@ -628,17 +631,21 @@ private void removeWeight(KmerPathNode node, List<List<KmerNode>> toRemove, Set<
 		assert(node.length() >= toRemove.size());
 		// remove from graph
 		removeFromGraph(node, includeMemoizationRemoval);
-		simplifyCandidates.addAll(node.next());
-		simplifyCandidates.addAll(node.prev());
-		simplifyCandidates.remove(node);
+		if (SIMPLIFY_AFTER_REMOVAL) {
+			simplifyCandidates.addAll(node.next());
+			simplifyCandidates.addAll(node.prev());
+			simplifyCandidates.remove(node);
+		}
 		Collection<KmerPathNode> replacementNodes = KmerPathNode.removeWeight(node, toRemove);
 		for (KmerPathNode split : replacementNodes) {
 			if (Defaults.SANITY_CHECK_DE_BRUIJN) {
 				assert(evidenceTracker.matchesExpected(new KmerPathSubnode(split)));
 			}
 			addToGraph(split);
 		}
-		simplifyCandidates.addAll(replacementNodes);
+		if (SIMPLIFY_AFTER_REMOVAL) {
+			simplifyCandidates.addAll(replacementNodes);
+		}
 	}
 	private void addToGraph(KmerPathNode node) {
 		boolean added = graphByPosition.add(node);

diff --git a/src/test/java/au/edu/wehi/idsv/debruijn/positional/NonReferenceContigAssemblerTest.java b/src/test/java/au/edu/wehi/idsv/debruijn/positional/NonReferenceContigAssemblerTest.java
@@ -368,7 +368,7 @@ public void should_remove_misassembled_partial_paths() {
 		pc.getAssemblyParameters().maxExpectedBreakendLengthMultiple = 1;
 		List<DirectedEvidence> e = new ArrayList<>();
 		for (int i = 1; i < 100; i++) {
-			e.add(SCE(FWD, ses, withReadName(String.format("%d-%d", 0, i), withSequence("TAAAAAAAAAAAAAAAAAAA", Read(0, i*10, "4M16S")))[0]));
+			e.add(SCE(FWD, ses, withReadName(String.format("%d-%d", 0, i), withSequence("TAAAAAAAAAAAAAAAAAAAAAAAAAAAA", Read(0, i*20, "4M25S")))[0]));
 		}
 		List<SAMRecord> output = go(pc, false, e.toArray(new DirectedEvidence[0]));
 		// the rest should have been removed