From 9e32d3f774697aac6653cbe5f162105420aed954 Mon Sep 17 00:00:00 2001
From: Charles Shale <shalecharles@gmail.com>
Date: Wed, 6 Mar 2024 16:06:50 +1100
Subject: [PATCH] Sage: added artefact unit test, bumped version

---
 pom.xml                                       |  2 +-
 .../hmftools/sage/evidence/ArtefactsTest.java | 35 ++++++++++++++++++-
 2 files changed, 35 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index 985fe90065..cd14453c11 100644
--- a/pom.xml
+++ b/pom.xml
@@ -84,7 +84,7 @@
         <patient-db.version>5.34</patient-db.version>
         <pave.version>1.6</pave.version>
         <purple.version>4.0.2</purple.version>
-        <sage.version>3.4.1</sage.version>
+        <sage.version>3.4.2</sage.version>
         <sigs.version>1.2.1</sigs.version>
         <sv-prep.version>1.3</sv-prep.version>
         <sv-tools.version>1.0</sv-tools.version>
diff --git a/sage/src/test/java/com/hartwig/hmftools/sage/evidence/ArtefactsTest.java b/sage/src/test/java/com/hartwig/hmftools/sage/evidence/ArtefactsTest.java
index 206831e93a..ff43cefa19 100644
--- a/sage/src/test/java/com/hartwig/hmftools/sage/evidence/ArtefactsTest.java
+++ b/sage/src/test/java/com/hartwig/hmftools/sage/evidence/ArtefactsTest.java
@@ -259,6 +259,39 @@ record = buildSamRecord(20, cigar, readContextBases, new String(readQualities));
         assertEquals(lowQualBase, adjustedBaseQual);
     }
 
+    @Test
+    public void testSnvWithAdjacentInsert()
+    {
+        int pos = 115;
+        String leftFlank = "AAAATCAGGA";
+        String rightFlank = "AAAGGCAGAA";
+
+        SimpleVariant variant = new SimpleVariant(CHR_1, pos, "G", "T");
+
+        int varIndex = 15;
+        String readContextBases = leftFlank + "CTGTTTTTTTTTTTTTTTTTTA" + rightFlank;
+
+        IndexedBases indexBases = new IndexedBases(
+                pos, varIndex, leftFlank.length(),
+                readContextBases.length() - rightFlank.length() - 1, rightFlank.length(), readContextBases.getBytes());
+
+        ArtefactContext artefactContext = ArtefactContext.buildContext(variant, indexBases);
+        assertNotNull(artefactContext);
+
+        int readLength = readContextBases.length();
+        String cigar = format("%dM", readLength);
+        byte[] readQualities = buildDefaultBaseQuals(readLength);
+
+        byte lowQualBase = 10;
+        readQualities[varIndex-1] = lowQualBase;
+        SAMRecord record = buildSamRecord(20, cigar, readContextBases, new String(readQualities));
+        record.setReadNegativeStrandFlag(true);
+
+        byte adjustedBaseQual = artefactContext.findApplicableBaseQual(record, varIndex);
+
+        assertEquals(lowQualBase, adjustedBaseQual);
+    }
+
     @Test
     public void testSnvBeforeInsert()
     {
@@ -281,7 +314,7 @@ public void testSnvBeforeInsert()
         ReadContext readContext = new ReadContext(pos, "", 0, "", indexBases, false);
 
         IndexedBases indexedRefBases = new IndexedBases(100, 0, refBases.getBytes());
-        QualityCalculator qualityCalculator = new QualityCalculator(TEST_CONFIG, RECALIBRATION, indexedRefBases);
+        QualityCalculator qualityCalculator = new QualityCalculator(TEST_CONFIG.Quality, RECALIBRATION, indexedRefBases);
 
         ReadContextCounter rcCounter = new ReadContextCounter(
                 1, variant, readContext, VariantTier.PANEL, 100, 0,