feat: raise exception if CollectDuplexSeqMetrics run on consensus BAM

src/main/scala/com/fulcrumgenomics/bam/api/SamRecord.scala

@@ -27,6 +27,7 @@ package com.fulcrumgenomics.bam.api
 
 import com.fulcrumgenomics.FgBioDef._
 import com.fulcrumgenomics.alignment.Cigar
+import com.fulcrumgenomics.umi.ConsensusTags.PerRead.AllPerReadTags
 import htsjdk.samtools
 import htsjdk.samtools.SamPairUtil.PairOrientation
 import htsjdk.samtools._
@@ -269,6 +270,10 @@ trait SamRecord {
       SamPairUtil.getPairOrientation(this) == PairOrientation.FR
   }
 
+  def isConsensus: Boolean = {
+    AllPerReadTags.exists(this.contains)
+  }
+
   /** Clone method that does a "reasonably deep" clone. The bases and quals are cloned as is the attributes map,
     * though not the values in the attributes map. */
   override def clone(): SamRecord = {

src/main/scala/com/fulcrumgenomics/umi/CollectDuplexSeqMetrics.scala

@@ -340,6 +340,7 @@ class CollectDuplexSeqMetrics
 
       // Assign reads a random number between 0 and 1 inclusive based on their read name
       group.foreach { rec =>
+        if (rec.isConsensus) throw new IllegalArgumentException("Found consensus record. Expected UMI-grouped BAM")
         val intHash    = math.abs(this.hasher.hashUnencodedChars(rec.name))
         val doubleHash = intHash / MaxIntAsDouble
         rec.transientAttrs(HashKey) = doubleHash

src/test/scala/com/fulcrumgenomics/bam/api/SamRecordTest.scala

@@ -27,6 +27,7 @@ package com.fulcrumgenomics.bam.api
 import com.fulcrumgenomics.alignment.Cigar
 import com.fulcrumgenomics.testing.SamBuilder.{Minus, Plus}
 import com.fulcrumgenomics.testing.{SamBuilder, UnitSpec}
+import com.fulcrumgenomics.umi.ConsensusTags.PerRead.AllPerReadTags
 import htsjdk.samtools.TextCigarCodec
 import org.scalatest.OptionValues
 
@@ -289,4 +290,17 @@ class SamRecordTest extends UnitSpec with OptionValues {
     rec1.matesOverlap shouldBe None // Mate's start is not enclosed by rec, and mate's end cannot be determined
     rec2.matesOverlap.value shouldBe true // Mate's start is enclosed by rec, regardless of where mate end is
   }
+
+  "SamRecord.isConsensus" 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(_.isConsensus) shouldBe false
+    builder.addPair(start1=100, start2=100, unmapped2=true).exists(_.isConsensus) shouldBe false
+  }
+
+  it should "return true for reads with consensus tags" in {
+    val builder = new SamBuilder(sort=Some(SamOrder.Coordinate), readLength=10, baseQuality=20)
+    AllPerReadTags.forall(
+      tag => builder.addFrag(start=10, attrs=Map(tag -> 123)).exists(_.isConsensus)
+    ) shouldBe true
+  }
 }

src/test/scala/com/fulcrumgenomics/umi/CollectDuplexSeqMetricsTest.scala

@@ -32,6 +32,7 @@ import com.fulcrumgenomics.bam.api.SamOrder
 import com.fulcrumgenomics.commons.util.SimpleCounter
 import com.fulcrumgenomics.testing.SamBuilder.{Minus, Plus}
 import com.fulcrumgenomics.testing.{SamBuilder, UnitSpec}
+import com.fulcrumgenomics.umi.ConsensusTags.PerRead.AllPerReadTags
 import com.fulcrumgenomics.util.{Io, Metric, Rscript}
 import htsjdk.samtools.util.{Interval, IntervalList}
 import org.apache.commons.math3.distribution.NormalDistribution
@@ -41,6 +42,7 @@ import scala.math.{max, min}
 class CollectDuplexSeqMetricsTest extends UnitSpec {
   private val MI = "MI"
   private val RX = "RX"
+  private val aD = "aD"
 
   // Case class to hold pointers to all the outputs of CollectDuplexSeqMetrics
   private case class Outputs(families: Path, duplexFamilies: Path, umis: Path, duplexUmis: Path, yields: Path, plots: Path) {
@@ -312,6 +314,14 @@ class CollectDuplexSeqMetricsTest extends UnitSpec {
     duplexFamilies.find(f => f.ab_size == 6 && f.ba_size == 0).get.count shouldBe 1
   }
 
+  it should "raise an exception if consensus records are provided" in {
+    val builder = new SamBuilder(readLength=100, sort=Some(SamOrder.TemplateCoordinate))
+    AllPerReadTags.foreach {
+      tag => builder.addPair(contig=1, start1=1000, start2=1100, attrs=Map(RX -> "AAA-GGG", MI -> "1/A", tag -> 10))
+      an[IllegalArgumentException] shouldBe thrownBy { exec(builder) }
+    }
+  }
+
   "CollectDuplexSeqMetrics.updateUmiMetrics" should "not count duplex umis" in collector(duplex=false).foreach { c =>
     val builder = new SamBuilder(readLength=10)
     builder.addPair(start1=100, start2=200, attrs=Map(RX -> "AAA-CCC", MI -> "1/A"))