refactor: rename isConsensusRead to isFgbioStyleConsensus

fulcrumgenomics · Jul 24, 2024 · ea80c6c · ea80c6c
1 parent 04a51e9
commit ea80c6c
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git 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
@@ -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
@@ -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
   }
 }