PileupBuilder should not report insertions when checking the final ma…

…pped base before soft-clipping (#956) * Correct check for insertion to avoid counting soft-clipped bases * Add unit tests for soft-clipped positions Co-authored-by: Clint Valentine <[email protected]> * Update src/test/scala/com/fulcrumgenomics/bam/pileup/PileupBuilderTest.scala --------- Co-authored-by: Clint Valentine <[email protected]>
fulcrumgenomics · Jan 17, 2024 · afa634e · afa634e
1 parent abb741b
commit afa634e
Show file tree

Hide file tree

Showing 2 changed files with 16 additions and 2 deletions.
diff --git a/src/main/scala/com/fulcrumgenomics/bam/pileup/PileupBuilder.scala b/src/main/scala/com/fulcrumgenomics/bam/pileup/PileupBuilder.scala
@@ -215,8 +215,8 @@ trait PileupBuilder extends PileupParameters {
             testAndAdd(DeletionEntry(rec, deletionPosition - 1))
           } else { // This site must be a matched site within the read.
             testAndAdd(BaseEntry(rec, offset - 1))
-            // Also check to see if the subsequent base represents an insertion.
-            if (offset < rec.length - 1 && rec.refPosAtReadPos(offset + 1) == 0) testAndAdd(InsertionEntry(rec, offset))
+            // Also check to see if any subsequent base represents an insertion.
+            if (rec.end > pos && rec.refPosAtReadPos(offset + 1) == 0) testAndAdd(InsertionEntry(rec, offset))
           }
         }
       }

diff --git a/src/test/scala/com/fulcrumgenomics/bam/pileup/PileupBuilderTest.scala b/src/test/scala/com/fulcrumgenomics/bam/pileup/PileupBuilderTest.scala
@@ -127,6 +127,7 @@ class PileupBuilderTest extends UnitSpec {
       builder.addFrag(name = "q3", start = 101, cigar = "31M9I10M").foreach(_.bases = "G" * ReadLength)
       builder.addFrag(name = "q4", start = 101, cigar = "30M9D20M").foreach(_.bases = "T" * ReadLength)
       builder.addFrag(name = "q5", start = 141, cigar = "10I40M"  ).foreach(_.bases = "N" * ReadLength)
+      builder.addFrag(name = "q6", start = 201, cigar = "47M3S"   ).foreach(_.bases = "N" * ReadLength)
 
       val source = builder.toSource
       val piler  = PileupBuilder(source, accessPattern = accessPattern, mappedPairsOnly = false)
@@ -170,6 +171,19 @@ class PileupBuilderTest extends UnitSpec {
       p4.iterator.collect{ case x: InsertionEntry => x }.map(_.rec.name).next() shouldBe "q5"
       p4.baseIterator.toSeq should contain theSameElementsAs p4.withoutIndels.iterator.toSeq
 
+      // Locus with the remainder of a read that is soft-clipped
+      val p5 = piler.pileup(Chr1, 247)
+      p5.depth shouldBe 1
+      p5.iterator.size shouldBe 1 // should not report an insertion due to the remaining soft-clipped bases
+      p5.baseIterator.size shouldBe 1
+      p5.baseIterator.toSeq should contain theSameElementsAs p5.withoutIndels.iterator.toSeq
+
+      // Locus at the site of a single read that is soft-clipped
+      val p6 = piler.pileup(Chr1, 248)
+      p6.depth shouldBe 0
+      p6.iterator.size shouldBe 0
+      p6.baseIterator.size shouldBe 0
+      p6.baseIterator.toSeq should contain theSameElementsAs p6.withoutIndels.iterator.toSeq
       source.safelyClose()
       piler.safelyClose()
     }