Remove other_matches from UmiCorrectionMetrics

Author: clintval

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

@@ -60,7 +60,6 @@ object CorrectUmis {
     * @param perfect_matches The number of UMI sequences that were perfect matches to this UMI.
     * @param one_mismatch_matches The number of UMI sequences that matched with a single mismatch.
     * @param two_mismatch_matches The number of UMI sequences that matched with two mismatches.
-    * @param other_matches The number of UMI sequences that matched with three or more mismatches.
     * @param fraction_of_matches The fraction of all UMIs that matched or were corrected to this UMI.
     * @param representation The `total_matches` for this UMI divided by the _mean_ `total_matches` for all UMIs.
     */
@@ -69,7 +68,6 @@ object CorrectUmis {
                                   var perfect_matches: Count = 0,
                                   var one_mismatch_matches: Count = 0,
                                   var two_mismatch_matches: Count = 0,
-                                  var other_matches: Count = 0,
                                   var fraction_of_matches: Proportion = 0,
                                   var representation: Double = 0
                                  ) extends Metric
@@ -223,7 +221,7 @@ class CorrectUmis
                   case 0 => metric.perfect_matches      += 1
                   case 1 => metric.one_mismatch_matches += 1
                   case 2 => metric.two_mismatch_matches += 1
-                  case _ => metric.other_matches        += 1
+                  case _ => ()
                 }
               }
               else {

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

@@ -149,11 +149,11 @@ class CorrectUmisTest extends UnitSpec {
     readBamRecs(rejects).map(_.name) should contain theSameElementsAs Seq("q9", "q10")
 
     val metricsByUmi = Metric.read[UmiCorrectionMetrics](metrics).map(m => m.umi -> m).toMap
-    metricsByUmi("AAAAAA") shouldBe UmiCorrectionMetrics(umi="AAAAAA", total_matches=5, perfect_matches=2, one_mismatch_matches=1, two_mismatch_matches=1, other_matches=1, fraction_of_matches = 5/10.0, representation = (5/8.0) / (1/4d))
-    metricsByUmi("CCCCCC") shouldBe UmiCorrectionMetrics(umi="CCCCCC", total_matches=1, perfect_matches=1, one_mismatch_matches=0, two_mismatch_matches=0, other_matches=0, fraction_of_matches = 1/10.0, representation = (1/8.0) / (1/4d))
-    metricsByUmi("GGGGGG") shouldBe UmiCorrectionMetrics(umi="GGGGGG", total_matches=1, perfect_matches=1, one_mismatch_matches=0, two_mismatch_matches=0, other_matches=0, fraction_of_matches = 1/10.0, representation = (1/8.0) / (1/4d))
-    metricsByUmi("TTTTTT") shouldBe UmiCorrectionMetrics(umi="TTTTTT", total_matches=1, perfect_matches=1, one_mismatch_matches=0, two_mismatch_matches=0, other_matches=0, fraction_of_matches = 1/10.0, representation = (1/8.0) / (1/4d))
-    metricsByUmi("NNNNNN") shouldBe UmiCorrectionMetrics(umi="NNNNNN", total_matches=2, perfect_matches=0, one_mismatch_matches=0, two_mismatch_matches=0, other_matches=0, fraction_of_matches = 2/10.0, representation = (2/8.0) / (1/4d))
+    metricsByUmi("AAAAAA") shouldBe UmiCorrectionMetrics(umi="AAAAAA", total_matches=5, perfect_matches=2, one_mismatch_matches=1, two_mismatch_matches=1, fraction_of_matches = 5/10.0, representation = (5/8.0) / (1/4d))
+    metricsByUmi("CCCCCC") shouldBe UmiCorrectionMetrics(umi="CCCCCC", total_matches=1, perfect_matches=1, one_mismatch_matches=0, two_mismatch_matches=0, fraction_of_matches = 1/10.0, representation = (1/8.0) / (1/4d))
+    metricsByUmi("GGGGGG") shouldBe UmiCorrectionMetrics(umi="GGGGGG", total_matches=1, perfect_matches=1, one_mismatch_matches=0, two_mismatch_matches=0, fraction_of_matches = 1/10.0, representation = (1/8.0) / (1/4d))
+    metricsByUmi("TTTTTT") shouldBe UmiCorrectionMetrics(umi="TTTTTT", total_matches=1, perfect_matches=1, one_mismatch_matches=0, two_mismatch_matches=0, fraction_of_matches = 1/10.0, representation = (1/8.0) / (1/4d))
+    metricsByUmi("NNNNNN") shouldBe UmiCorrectionMetrics(umi="NNNNNN", total_matches=2, perfect_matches=0, one_mismatch_matches=0, two_mismatch_matches=0, fraction_of_matches = 2/10.0, representation = (2/8.0) / (1/4d))
   }
 
   it should "run end to end and do the right thing for a handful of fragments with duplex UMIs" in {
@@ -177,11 +177,11 @@ class CorrectUmisTest extends UnitSpec {
     readBamRecs(rejects).map(_.name) should contain theSameElementsAs Seq("q3", "q5")
 
     val metricsByUmi = Metric.read[UmiCorrectionMetrics](metrics).map(m => m.umi -> m).toMap
-    metricsByUmi("AAAAAA") shouldBe UmiCorrectionMetrics(umi="AAAAAA", total_matches=3, perfect_matches=2, one_mismatch_matches=1, two_mismatch_matches=0, other_matches=0, fraction_of_matches = 3/10.0, representation = (3/8.0) / (1/4d))
-    metricsByUmi("CCCCCC") shouldBe UmiCorrectionMetrics(umi="CCCCCC", total_matches=2, perfect_matches=1, one_mismatch_matches=1, two_mismatch_matches=0, other_matches=0, fraction_of_matches = 2/10.0, representation = (2/8.0) / (1/4d))
-    metricsByUmi("GGGGGG") shouldBe UmiCorrectionMetrics(umi="GGGGGG", total_matches=1, perfect_matches=1, one_mismatch_matches=0, two_mismatch_matches=0, other_matches=0, fraction_of_matches = 1/10.0, representation = (1/8.0) / (1/4d))
-    metricsByUmi("TTTTTT") shouldBe UmiCorrectionMetrics(umi="TTTTTT", total_matches=2, perfect_matches=2, one_mismatch_matches=0, two_mismatch_matches=0, other_matches=0, fraction_of_matches = 2/10.0, representation = (2/8.0) / (1/4d))
-    metricsByUmi("NNNNNN") shouldBe UmiCorrectionMetrics(umi="NNNNNN", total_matches=2, perfect_matches=0, one_mismatch_matches=0, two_mismatch_matches=0, other_matches=0, fraction_of_matches = 2/10.0, representation = (2/8.0) / (1/4d))
+    metricsByUmi("AAAAAA") shouldBe UmiCorrectionMetrics(umi="AAAAAA", total_matches=3, perfect_matches=2, one_mismatch_matches=1, two_mismatch_matches=0, fraction_of_matches = 3/10.0, representation = (3/8.0) / (1/4d))
+    metricsByUmi("CCCCCC") shouldBe UmiCorrectionMetrics(umi="CCCCCC", total_matches=2, perfect_matches=1, one_mismatch_matches=1, two_mismatch_matches=0, fraction_of_matches = 2/10.0, representation = (2/8.0) / (1/4d))
+    metricsByUmi("GGGGGG") shouldBe UmiCorrectionMetrics(umi="GGGGGG", total_matches=1, perfect_matches=1, one_mismatch_matches=0, two_mismatch_matches=0, fraction_of_matches = 1/10.0, representation = (1/8.0) / (1/4d))
+    metricsByUmi("TTTTTT") shouldBe UmiCorrectionMetrics(umi="TTTTTT", total_matches=2, perfect_matches=2, one_mismatch_matches=0, two_mismatch_matches=0, fraction_of_matches = 2/10.0, representation = (2/8.0) / (1/4d))
+    metricsByUmi("NNNNNN") shouldBe UmiCorrectionMetrics(umi="NNNNNN", total_matches=2, perfect_matches=0, one_mismatch_matches=0, two_mismatch_matches=0, fraction_of_matches = 2/10.0, representation = (2/8.0) / (1/4d))
   }
 
   it should "do the same thing whether the UMIs are on the command line or in a file" in {