Fix a bug that have scores at same position counted multiple times

Author: philiptzou

NGS/gradle/wrapper/gradle-wrapper.jar

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.10-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.6.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

NGS/gradle/wrapper/gradle-wrapper.properties

@@ -74,7 +74,7 @@ test {
 }
 
 jacocoTestReport {
-    classDirectories =  files(jacocoReportClasses)
+    classDirectories.from = files(jacocoReportClasses)
     reports {
         xml.enabled = true
         html.enabled = true

asi_interpreter

@@ -22,7 +22,9 @@
 //import static org.mockito.Mockito.*;
 
 import java.util.Collections;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import java.util.TreeSet;
 
@@ -278,6 +280,16 @@ public void testGetDrugSuscsCase1() {
 		assertFalse(geneDR.getMutScores(hiv.getDrug("NVP")).isEmpty());
 	}
 
+	@Test
+	public void testGetMutScores$UseMaxScore() {
+		MutationSet<HIV> mutations = MutationSet.parseString(hiv.getGene("HIV1RT"), "RT184IV");
+		DrugResistanceAlgorithm<HIV> algorithm = hiv.getDrugResistAlgorithm("HIVDB_8.9");
+		GeneDR<HIV> geneDR = new GeneDR<HIV>(hiv.getGene("HIV1RT"), mutations, algorithm);
+		Map<MutationSet<HIV>, Double> expects = new HashMap<>();
+		expects.put(mutations, -10.0);
+		assertEquals(expects, geneDR.getDrugSusc(hiv.getDrug("AZT")).getPartialScores());
+	}
+	
 	@Test
 	public void testGetComboMutScores$Drug() {
 		MutationSet<HIV> mutations = MutationSet.parseString(hiv.getGene("HIV1RT"), "RT101E, RT181C");