test: update tests

PharmGKB · Feb 28, 2025 · ec65d4b · ec65d4b
1 parent 5ff5649
commit ec65d4b
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/src/test/java/org/pharmgkb/pharmcat/haplotype/NamedAlleleMatcherTest.java b/src/test/java/org/pharmgkb/pharmcat/haplotype/NamedAlleleMatcherTest.java
@@ -247,7 +247,7 @@ void sortException() throws Exception {
       System.out.println("\t" + result.getVcfWarnings().get(key));
     }
 
-    assertEquals(78, result.getVcfWarnings().size());
+    assertEquals(34, result.getVcfWarnings().size());
     GeneCall rez = result.getGeneCalls().stream().filter(g -> g.getGene().equals("CYP2D6"))
         .findAny()
         .orElseThrow(() -> new IllegalStateException("CYP2D6 not called"));

diff --git a/src/test/java/org/pharmgkb/pharmcat/reporter/format/CallsOnlyFormatTest.java b/src/test/java/org/pharmgkb/pharmcat/reporter/format/CallsOnlyFormatTest.java
@@ -101,7 +101,7 @@ void multipleDiplotypes(TestInfo testInfo) throws Exception {
     System.out.println("normal");
     System.out.println(normalTsv);
     String[] lines = normalTsv.split("\n");
-    assertEquals(3, lines.length);
+    assertEquals(4, lines.length);
     Map<String, List<String>> geneMap = parseTsv(lines, 16, "CYP2C19", "DPYD");
     assertEquals(1, geneMap.get("CYP2C19").size());
     assertEquals(1, geneMap.get("DPYD").size());
@@ -170,7 +170,7 @@ void withDebugInfo(TestInfo testInfo) throws Exception {
       System.out.println("normal");
       System.out.println(normalTsv);
       String[] lines = normalTsv.split("\n");
-      assertEquals(10, lines.length);
+      assertEquals(11, lines.length);
       Map<String, List<String>> geneMap = parseTsv(lines, 18, genes);
       assertEquals(1, geneMap.get("CYP2C19").size());
       assertEquals(1, geneMap.get("DPYD").size());
@@ -248,6 +248,9 @@ private SortedMap<String, List<String>> parseTsv(String[] lines, int maxColumns,
     // test normal
     SortedMap<String, List<String>> geneMap = new TreeMap<>();
     for (String line : lines) {
+      if (line.startsWith("PharmCAT") || line.startsWith("Gene\t") || line.startsWith("Sample ID\t")) {
+        continue;
+      }
       String[] data = line.split("\t");
       if (data.length != maxColumns) {
         StringBuilder builder = new StringBuilder();