diff --git a/src/main/scala/com/fulcrumgenomics/umi/CollectDuplexSeqMetrics.scala b/src/main/scala/com/fulcrumgenomics/umi/CollectDuplexSeqMetrics.scala index 891e93d40..30d807a7c 100644 --- a/src/main/scala/com/fulcrumgenomics/umi/CollectDuplexSeqMetrics.scala +++ b/src/main/scala/com/fulcrumgenomics/umi/CollectDuplexSeqMetrics.scala @@ -318,7 +318,7 @@ class CollectDuplexSeqMetrics "prior to consensus calling. The UMI-grouped BAM is the output of running GroupReadsByUmi." + s"\nFirst record in $input has consensus SAM tags present:\n$rec" - if (Umis.isConsensusRead(rec)) throw new IllegalArgumentException(exceptionString) + if (Umis.isFgbioStyleConsensus(rec)) throw new IllegalArgumentException(exceptionString) } val iterator = intervals match { case None => _filteredIterator diff --git a/src/main/scala/com/fulcrumgenomics/umi/Umis.scala b/src/main/scala/com/fulcrumgenomics/umi/Umis.scala index a024dfc2f..63cb4e3f7 100644 --- a/src/main/scala/com/fulcrumgenomics/umi/Umis.scala +++ b/src/main/scala/com/fulcrumgenomics/umi/Umis.scala @@ -134,7 +134,7 @@ object Umis { * @param rec the record to test * @return boolean indicating if the record is a consensus or not */ - def isConsensusRead(rec: SamRecord): Boolean = { + def isFgbioStyleConsensus(rec: SamRecord): Boolean = { rec.contains(ConsensusTags.PerRead.RawReadCount) || (rec.contains(ConsensusTags.PerRead.AbRawReadCount) && rec.contains(ConsensusTags.PerRead.BaRawReadCount)) } diff --git a/src/test/scala/com/fulcrumgenomics/umi/UmisTest.scala b/src/test/scala/com/fulcrumgenomics/umi/UmisTest.scala index 8ffeffcc6..d469aa168 100644 --- a/src/test/scala/com/fulcrumgenomics/umi/UmisTest.scala +++ b/src/test/scala/com/fulcrumgenomics/umi/UmisTest.scala @@ -114,17 +114,17 @@ class UmisTest extends UnitSpec with OptionValues { "Umis.isConsensusRead" should "return false for reads without consensus tags" in { val builder = new SamBuilder(sort=Some(SamOrder.Coordinate), readLength=10, baseQuality=20) - builder.addFrag(start=100).exists(Umis.isConsensusRead) shouldBe false - builder.addPair(start1=100, start2=100, unmapped2=true).exists(Umis.isConsensusRead) shouldBe false + builder.addFrag(start=100).exists(Umis.isFgbioStyleConsensus) shouldBe false + builder.addPair(start1=100, start2=100, unmapped2=true).exists(Umis.isFgbioStyleConsensus) shouldBe false } it should "return true for reads with consensus tags" in { val builder = new SamBuilder(sort=Some(SamOrder.Coordinate), readLength=10, baseQuality=20) builder.addFrag(start=10, attrs=Map(ConsensusTags.PerRead.RawReadCount -> 10)) - .exists(Umis.isConsensusRead) shouldBe true + .exists(Umis.isFgbioStyleConsensus) shouldBe true builder.addFrag( start=10, attrs=Map(ConsensusTags.PerRead.AbRawReadCount -> 10, ConsensusTags.PerRead.BaRawReadCount -> 10) - ).exists(Umis.isConsensusRead) shouldBe true + ).exists(Umis.isFgbioStyleConsensus) shouldBe true } }