From f4fe35ae5647af6b52c87aa4028e1d3c42f40cd6 Mon Sep 17 00:00:00 2001
From: Mark Woon <markwoon@gmail.com>
Date: Fri, 26 Jul 2024 14:42:45 -0700
Subject: [PATCH] fix(namedallelematcher): avoid exceptions

---
 .../pharmcat/haplotype/DpydHapB3Matcher.java  |  4 +-
 .../pharmcat/haplotype/model/BaseMatch.java   |  2 +-
 .../java/org/pharmgkb/pharmcat/DpydTest.java  | 61 +++++++++++++++++++
 3 files changed, 64 insertions(+), 3 deletions(-)

diff --git a/src/main/java/org/pharmgkb/pharmcat/haplotype/DpydHapB3Matcher.java b/src/main/java/org/pharmgkb/pharmcat/haplotype/DpydHapB3Matcher.java
index da221e20..bd493b57 100644
--- a/src/main/java/org/pharmgkb/pharmcat/haplotype/DpydHapB3Matcher.java
+++ b/src/main/java/org/pharmgkb/pharmcat/haplotype/DpydHapB3Matcher.java
@@ -247,8 +247,8 @@ public SortedSet<DiplotypeMatch> mergePhasedDiplotypeMatch(MatchData matchData,
     BaseMatch h2 = dm.getHaplotype2();
 
     boolean isHapB3homozygous = m_numHapB3Called == 2 && (
-        m_hapB3Call.stream().filter(c -> c.equals("1")).count() == 2 ||
-            m_hapB3IntronCall.stream().filter(c -> c.equals("1")).count() == 2
+        (m_hapB3Call == null || m_hapB3Call.stream().filter(c -> c.equals("1")).count() == 2) ||
+            (m_hapB3IntronCall == null || m_hapB3IntronCall.stream().filter(c -> c.equals("1")).count() == 2)
     );
 
     if (dm.getHaplotype1().getName().equals(dm.getHaplotype2().getName()) || isHapB3homozygous) {
diff --git a/src/main/java/org/pharmgkb/pharmcat/haplotype/model/BaseMatch.java b/src/main/java/org/pharmgkb/pharmcat/haplotype/model/BaseMatch.java
index 73ccdccb..2800390c 100644
--- a/src/main/java/org/pharmgkb/pharmcat/haplotype/model/BaseMatch.java
+++ b/src/main/java/org/pharmgkb/pharmcat/haplotype/model/BaseMatch.java
@@ -22,7 +22,7 @@
  *
  * @author Mark Woon
  */
-public abstract class BaseMatch implements Comparable<BaseMatch> {
+public class BaseMatch implements Comparable<BaseMatch> {
   @Expose
   @SerializedName("name")
   private String m_name;
diff --git a/src/test/java/org/pharmgkb/pharmcat/DpydTest.java b/src/test/java/org/pharmgkb/pharmcat/DpydTest.java
index 96aa45d5..7c8329a7 100644
--- a/src/test/java/org/pharmgkb/pharmcat/DpydTest.java
+++ b/src/test/java/org/pharmgkb/pharmcat/DpydTest.java
@@ -731,6 +731,67 @@ void testFindCombinations(TestInfo testInfo) throws Exception {
   }
 
 
+  @Test
+  void hapB3AndIntronicC(TestInfo testInfo) throws Exception {
+
+    PipelineWrapper testWrapper = new PipelineWrapper(testInfo, true, false, false);
+    testWrapper.getVcfBuilder()
+        .phased()
+        // hapB3 exon C>T
+        .variation("DPYD", "rs56038477", "C", "T")
+        // hapB3 intron G>C
+        .variation("DPYD", "rs75017182", "C", "C")
+    ;
+
+    Path vcfFile = testWrapper.execute();
+
+    List<String> expectedCalls = List.of(
+        "c.1129-5923C>G/c.1129-5923C>G, c.1236G>A (HapB3)"
+    );
+    RecPresence hasDpwgAnnotations = RecPresence.YES;
+
+    testWrapper.testCalledByMatcher("DPYD");
+    testWrapper.testSourceDiplotypes(DataSource.CPIC, "DPYD", expectedCalls);
+    testWrapper.testRecommendedDiplotypes(DataSource.CPIC, "DPYD", List.of("c.1129-5923C>G, c.1236G>A (HapB3)", "c.1129-5923C>G"));
+    testWrapper.testPrintCalls(DataSource.CPIC, "DPYD", expectedCalls);
+
+    dpydHasReports(testWrapper, hasDpwgAnnotations);
+
+    Document document = readHtmlReport(vcfFile);
+    dpydHtmlChecks(document, expectedCalls, false, hasDpwgAnnotations);
+  }
+
+  @Test
+  void hapB3AndIntronicD(TestInfo testInfo) throws Exception {
+
+    PipelineWrapper testWrapper = new PipelineWrapper(testInfo, true, false, false);
+    testWrapper.getVcfBuilder()
+        .phased()
+        // hapB3 exon C>T
+        .variation("DPYD", "rs56038477", "T", "C")
+        // hapB3 intron G>C
+        .variation("DPYD", "rs75017182", "C", "C")
+    ;
+
+    Path vcfFile = testWrapper.execute();
+
+    List<String> expectedCalls = List.of(
+        "c.1129-5923C>G/c.1129-5923C>G, c.1236G>A (HapB3)"
+    );
+    RecPresence hasDpwgAnnotations = RecPresence.YES;
+
+    testWrapper.testCalledByMatcher("DPYD");
+    testWrapper.testSourceDiplotypes(DataSource.CPIC, "DPYD", expectedCalls);
+    testWrapper.testRecommendedDiplotypes(DataSource.CPIC, "DPYD", List.of("c.1129-5923C>G, c.1236G>A (HapB3)", "c.1129-5923C>G"));
+    testWrapper.testPrintCalls(DataSource.CPIC, "DPYD", expectedCalls);
+
+    dpydHasReports(testWrapper, hasDpwgAnnotations);
+
+    Document document = readHtmlReport(vcfFile);
+    dpydHtmlChecks(document, expectedCalls, false, hasDpwgAnnotations);
+  }
+
+
   @Test
   void hapB3(TestInfo testInfo) throws Exception {