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OffTargetDetector should not pass primer pairs when no amplicons are … #6

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OffTargetDetector should not pass primer pairs when no amplicons are … #6

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OffTargetDetector should not pass primer pairs when no amplicons are …
nh13 Aug 8, 2024
875fc77
Update OffTargetDetector.scala
nh13 Aug 10, 2024
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20 changes: 13 additions & 7 deletions src/main/scala/com/fulcrumgenomics/primerdesign/offtarget/OffTargetDetector.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -166,13 +166,19 @@ class OffTargetDetector(val bwaExecutable: FilePath = BwaAlnInteractive.DefaultB
else {
val amps = toAmplicons(p1.hits, p2.hits, this.maxAmpliconSize)

OffTargetResult(
primerPair = pp,
passes = amps.lengthCompare(maxPrimerPairHits) <= 0,
mappings = if (keepMappings) amps else Seq.empty,
leftPrimerMappings = if (keepPrimerMappings) p1.hits.map(hitToMapping) else Seq.empty,
rightPrimerMappings = if (keepPrimerMappings) p2.hits.map(hitToMapping) else Seq.empty
)
// In some cases, when map left and right primers independently and they multi-map, sometimes `bwa` may not return a mapping to the
// "on-target" (designed) location, and if none of the other combinations generate ("amplifiable") amplicons, then there are no
// off-target amplicons. In such a case, we return an empty OffTargetResult
if (amps.isEmpty) OffTargetResult(primerPair=pp, passes=false, mappings=Nil)
else {
OffTargetResult(
primerPair = pp,
passes = amps.lengthCompare(maxPrimerPairHits) <= 0,
mappings = if (keepMappings) amps else Seq.empty,
leftPrimerMappings = if (keepPrimerMappings) p1.hits.map(hitToMapping) else Seq.empty,
rightPrimerMappings = if (keepPrimerMappings) p2.hits.map(hitToMapping) else Seq.empty
)
}
}

progress.foreach(_.record())
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