From 3f2b707ad64d03a6b8f97f753f727a27a481cdf1 Mon Sep 17 00:00:00 2001
From: Matthew Mah <mmah@broadinstitute.org>
Date: Thu, 2 Nov 2023 14:45:42 -0400
Subject: [PATCH] Fix off by 1 error on merge lengths. Cleanups for warnings.

---
 pom.xml                                       |  2 +-
 .../adnascreen/IndexAndBarcodeScreener.java   |  2 +-
 src/main/java/adnascreen/Read.java            |  2 +-
 .../java/adnascreen/SampleSetsCounter.java    |  1 -
 src/test/java/adnascreen/MergeTests.java      | 26 +++++++++++++++++++
 5 files changed, 29 insertions(+), 4 deletions(-)

diff --git a/pom.xml b/pom.xml
index 599fc4d..d2f4cbd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -2,7 +2,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>edu.harvard.hms.reichlab</groupId>
   <artifactId>adnascreen</artifactId>
-  <version>1.11.4-SNAPSHOT</version>
+  <version>1.11.5-SNAPSHOT</version>
   <name>Ancient DNA Tools</name>
   <properties>
    <maven.compiler.source>1.8</maven.compiler.source>
diff --git a/src/main/java/adnascreen/IndexAndBarcodeScreener.java b/src/main/java/adnascreen/IndexAndBarcodeScreener.java
index 14648bc..5de0c6a 100644
--- a/src/main/java/adnascreen/IndexAndBarcodeScreener.java
+++ b/src/main/java/adnascreen/IndexAndBarcodeScreener.java
@@ -283,7 +283,7 @@ public Boolean call() throws IOException, InterruptedException{
 				try {
 					// queue each paired read for merging
 					enqueuePairedReads(pool, resultsQueue, r1Filename, r2Filename, i1Filename, i2Filename, i5Label, i7Label);
-					return new Boolean(true);
+					return Boolean.TRUE;
 				} catch (IOException | InterruptedException e) {
 					throw(e);
 				} finally {
diff --git a/src/main/java/adnascreen/Read.java b/src/main/java/adnascreen/Read.java
index 248164e..e64ec59 100644
--- a/src/main/java/adnascreen/Read.java
+++ b/src/main/java/adnascreen/Read.java
@@ -162,7 +162,7 @@ public static List<Integer> findBestAlignment(Read a, Read b, int maxPenalty, in
 		// bbbbbbbbbbb
 		// starting position is for minimum required overlap
 		// ending position is for minimum result length
-		for(int offset = a.length() - minOverlapLength; b.length() + offset > minResultLength; offset--){
+		for(int offset = a.length() - minOverlapLength; b.length() + offset >= minResultLength; offset--){
 			int aOffset, bOffset;
 			if(offset >= 0){
 				aOffset = offset;
diff --git a/src/main/java/adnascreen/SampleSetsCounter.java b/src/main/java/adnascreen/SampleSetsCounter.java
index 9f00a08..c323fe9 100644
--- a/src/main/java/adnascreen/SampleSetsCounter.java
+++ b/src/main/java/adnascreen/SampleSetsCounter.java
@@ -7,7 +7,6 @@
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.Map;
-import java.util.Set;
 import java.util.stream.Stream;
 
 /**
diff --git a/src/test/java/adnascreen/MergeTests.java b/src/test/java/adnascreen/MergeTests.java
index 8031705..d6d7d4f 100644
--- a/src/test/java/adnascreen/MergeTests.java
+++ b/src/test/java/adnascreen/MergeTests.java
@@ -60,6 +60,32 @@ public void duplicateAlignment(){
 		assertEquals(0, offset);
 	}
 	
+	@Test
+	public void duplicateAlignmentMinLength(){
+		// reads minus barcodes
+		Read r1 = new Read("@NS500217:348:HTW2FBGXY:1:11101:22352:1064 1:N:0:0",
+				"CTAGCATTACTTATATGATATGTCTCCATA",
+				"EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE");
+		
+		List<Integer> alignments = Read.findBestAlignment(r1, r1, maxPenalty, minOverlapLength, minResultLength, maxPositions,
+				mismatchPenaltyHigh, mismatchPenaltyLow, mismatchBaseQualityThreshold);
+		assertEquals(1, alignments.size());
+		int offset = alignments.get(0);
+		assertEquals(0, offset);
+	}
+	
+	@Test
+	public void duplicateAlignmentBelowMinLength(){
+		// reads minus barcodes
+		Read r1 = new Read("@NS500217:348:HTW2FBGXY:1:11101:22352:1064 1:N:0:0",
+				"CTAGCATTACTTATATGATATGTCTCCAT",
+				"EEEEEEEEEEEEEEEEEEEEEEEEEEEEE");
+		
+		List<Integer> alignments = Read.findBestAlignment(r1, r1, maxPenalty, minOverlapLength, minResultLength, maxPositions,
+				mismatchPenaltyHigh, mismatchPenaltyLow, mismatchBaseQualityThreshold);
+		assertEquals(0, alignments.size());
+	}
+	
 	@Test
 	public void testTrimTrailingN(){
 		Read r1 = new Read("@NS500217:348:HTW2FBGXY:1:11101:22352:1064 1:N:0:0",