From fe7ea29709ac69dd9dc4e107a0427adf6f28c289 Mon Sep 17 00:00:00 2001 From: mozack Date: Mon, 14 Sep 2020 12:30:49 -0400 Subject: [PATCH] Upped to version 2.23. --- src/main/java/abra/JunctionUtils.java | 2 +- src/main/java/abra/NativeSemiGlobalAligner.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/java/abra/JunctionUtils.java b/src/main/java/abra/JunctionUtils.java index d8f93ae..cc1d25e 100644 --- a/src/main/java/abra/JunctionUtils.java +++ b/src/main/java/abra/JunctionUtils.java @@ -397,7 +397,7 @@ public static JunctionSequence getSequenceForJunctions(List 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 index 0fedcb8..b3437fa 100644 --- 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;