Upped to version 2.23.

mozack · Sep 14, 2020 · fe7ea29 · fe7ea29
1 parent 7b79be3
commit fe7ea29
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/src/main/java/abra/JunctionUtils.java b/src/main/java/abra/JunctionUtils.java
@@ -397,7 +397,7 @@ public static JunctionSequence getSequenceForJunctions(List<Feature> junctions,
 				String rightSeq = c2r.getSequence(chromosome, rightStart, rightStop-rightStart);
 				juncSeq.append(rightSeq);
 				// Junction pos and length should already be added
-				if (juncSeq.length() > ReAligner.MAX_REF_REGION_LEN) {
+				if (juncSeq.length() > NativeSemiGlobalAligner.MAX_REF_LEN) {
 					// Make sure we don't blow up the hardcoded size C matrix
 					Logger.warn("Junction Ref Seq to long: " + juncSeq.toString());
 

diff --git a/src/main/java/abra/NativeSemiGlobalAligner.java b/src/main/java/abra/NativeSemiGlobalAligner.java
@@ -11,8 +11,8 @@ public class NativeSemiGlobalAligner {
 	private int gapOpen = -48;
 	private int gapExtend = -1;
 
-	private static final int MAX_CONTIG_LEN = 1998;
-	private static final int MAX_REF_LEN = 4998;
+	public static final int MAX_CONTIG_LEN = 1998;
+	public static final int MAX_REF_LEN = 4998;
 
 	public NativeSemiGlobalAligner(int match, int mismatch, int gapOpen, int gapExtend) {
 		this.match = match;