Fix off by 1 error on merge lengths. Cleanups for warnings.

DReichLab · Nov 2, 2023 · 3f2b707 · 3f2b707
1 parent 50d89e5
commit 3f2b707
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Showing 5 changed files with 29 additions and 4 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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",