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PileupBuilder should not report insertions when checking the final mapped base before soft-clipping #956

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merged 3 commits into from
Jan 17, 2024
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PileupBuilder should not report insertions when checking the final mapped base before soft-clipping #956

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7b91eb6
Correct check for insertion to avoid counting soft-clipped bases
jrm5100 Jan 5, 2024
a17217d
add unit tests for soft-clipped positions
jrm5100 Jan 17, 2024
bc462fb
Update src/test/scala/com/fulcrumgenomics/bam/pileup/PileupBuilderTes…
clintval Jan 17, 2024
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4 changes: 2 additions & 2 deletions src/main/scala/com/fulcrumgenomics/bam/pileup/PileupBuilder.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -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))
}
}
}
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14 changes: 14 additions & 0 deletions src/test/scala/com/fulcrumgenomics/bam/pileup/PileupBuilderTest.scala
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Expand Up @@ -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)
Expand Down Expand Up @@ -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 p5.withoutIndels.iterator.toSeq
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source.safelyClose()
piler.safelyClose()
}
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