refactor: only import ConsensusTags

fulcrumgenomics · Jul 24, 2024 · c015aef · c015aef
1 parent 97c52ac
commit c015aef
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Showing 3 changed files with 16 additions and 10 deletions.
diff --git a/src/main/scala/com/fulcrumgenomics/umi/Umis.scala b/src/main/scala/com/fulcrumgenomics/umi/Umis.scala
@@ -26,8 +26,7 @@
 package com.fulcrumgenomics.umi
 
 import com.fulcrumgenomics.bam.api.SamRecord
-import com.fulcrumgenomics.umi.ConsensusTags.PerBase.AbRawReadCount
-import com.fulcrumgenomics.umi.ConsensusTags.PerRead.{BaRawReadCount, RawReadCount}
+import com.fulcrumgenomics.umi.ConsensusTags
 import com.fulcrumgenomics.util.Sequences
 
 object Umis {
@@ -136,6 +135,7 @@ object Umis {
    * @return boolean indicating if the record is a consensus or not
    */
   def isConsensusRead(rec: SamRecord): Boolean = {
-    rec.contains(RawReadCount) | (rec.contains(AbRawReadCount) & rec.contains(BaRawReadCount))
+    rec.contains(ConsensusTags.PerRead.RawReadCount) ||
+      (rec.contains(ConsensusTags.PerRead.AbRawReadCount) && rec.contains(ConsensusTags.PerRead.BaRawReadCount))
   }
 }
diff --git a/src/test/scala/com/fulcrumgenomics/umi/CollectDuplexSeqMetricsTest.scala b/src/test/scala/com/fulcrumgenomics/umi/CollectDuplexSeqMetricsTest.scala
@@ -31,8 +31,7 @@ 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.PerBase.AbRawReadCount
-import com.fulcrumgenomics.umi.ConsensusTags.PerRead.{AllPerReadTags, BaRawReadCount}
+import com.fulcrumgenomics.umi.ConsensusTags
 import com.fulcrumgenomics.util.{Io, Metric, Rscript}
 import htsjdk.samtools.util.{Interval, IntervalList}
 import org.apache.commons.math3.distribution.NormalDistribution
@@ -320,7 +319,12 @@ class CollectDuplexSeqMetricsTest extends UnitSpec {
       contig=1,
       start1=1000,
       start2=1100,
-      attrs=Map(RX -> "AAA-GGG", MI -> "1/A", AbRawReadCount -> 10, BaRawReadCount -> 10)
+      attrs=Map(
+        RX -> "AAA-GGG",
+        MI -> "1/A",
+        ConsensusTags.PerRead.AbRawReadCount -> 10,
+        ConsensusTags.PerRead.BaRawReadCount -> 10
+      )
     )
     an[IllegalArgumentException] shouldBe thrownBy { exec(builder) }
   }

diff --git a/src/test/scala/com/fulcrumgenomics/umi/UmisTest.scala b/src/test/scala/com/fulcrumgenomics/umi/UmisTest.scala
@@ -27,8 +27,7 @@ package com.fulcrumgenomics.umi
 
 import com.fulcrumgenomics.bam.api.{SamOrder, SamRecord}
 import com.fulcrumgenomics.testing.{SamBuilder, UnitSpec}
-import com.fulcrumgenomics.umi.ConsensusTags.PerBase.AbRawReadCount
-import com.fulcrumgenomics.umi.ConsensusTags.PerRead.{BaRawReadCount, RawReadCount}
+import com.fulcrumgenomics.umi.ConsensusTags
 import org.scalatest.OptionValues
 
 class UmisTest extends UnitSpec with OptionValues {
@@ -122,8 +121,11 @@ class UmisTest extends UnitSpec with OptionValues {
 
   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(RawReadCount -> 10)).exists(Umis.isConsensusRead) shouldBe true
-    builder.addFrag(start=10, attrs=Map(AbRawReadCount -> 10, BaRawReadCount -> 10))
+    builder.addFrag(start=10, attrs=Map(ConsensusTags.PerRead.RawReadCount -> 10))
       .exists(Umis.isConsensusRead) shouldBe true
+    builder.addFrag(
+        start=10,
+        attrs=Map(ConsensusTags.PerRead.AbRawReadCount -> 10, ConsensusTags.PerRead.BaRawReadCount -> 10)
+    ).exists(Umis.isConsensusRead) shouldBe true
   }
 }