Reverting unintended commit.

mozack · Jun 20, 2016 · dabd307 · dabd307
1 parent 543cc08
commit dabd307
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/src/main/java/abra/ReAligner.java b/src/main/java/abra/ReAligner.java
@@ -700,10 +700,10 @@ private boolean isAnyElementDifferent(List<String> elems) {
 	static List<Feature> getRegions(String regionsBed, int readLength, boolean hasPresetKmers) throws IOException {
 		RegionLoader loader = new RegionLoader();
 		List<Feature> regions = loader.load(regionsBed, hasPresetKmers);
-//		if (regions.size() > 0 && (regions.get(0).getKmer() == 0)) {
-//			regions = RegionLoader.collapseRegions(regions, readLength);
-//			regions = splitRegions(regions);
-//		}
+		if (regions.size() > 0 && (regions.get(0).getKmer() == 0)) {
+			regions = RegionLoader.collapseRegions(regions, readLength);
+			regions = splitRegions(regions);
+		}
 
 		return regions;
 	}
@@ -1055,7 +1055,7 @@ private NativeAssembler newAssembler(Feature region) {
 		assem.setMaxContigs(assemblerSettings
 				.getMaxPotentialContigs());
 
-		assem.setMaxPathsFromRoot(100000000);
+		assem.setMaxPathsFromRoot(100000);
 		assem.setReadLength(readLength);
 		//assem.setKmer(assemblerSettings.getKmerSize());
 		assem.setKmer(getKmers(region));