From ca81af8ad38ce04847af194ca77210978acb5040 Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Mon, 16 Dec 2024 11:26:19 -0800
Subject: [PATCH] refactor: variable names

---
 .../fulcrumgenomics/umi/GroupReadsByUmi.scala | 52 +++++++++----------
 1 file changed, 25 insertions(+), 27 deletions(-)

diff --git a/src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala b/src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala
index ddbcc9c71..615983593 100644
--- a/src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala
+++ b/src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala
@@ -468,17 +468,17 @@ case class TagFamilySizeMetric(family_size: Int,
 
 /**
  * Metrics produced by `GroupReadsByUmi` to describe reads passed through UMI grouping
- * @param reads The number of reads accepted for grouping
- * @param filteredNonPf The number of non-PF reads
- * @param filteredPoorAlignment The number of templates discarded for poor
- * @param filteredNsInUmi The number of templates discarded due to one or more Ns in the UMI
- * @param filterUmisTooShort The number of templates discarded due to a shorter than expected UMI
+ * @param sam_records The number of SAM records accepted for grouping.
+ * @param filtered_non_pf The number of non-PF SAM records.
+ * @param filtered_poor_alignment The number of SAM records discarded for poor alignment.
+ * @param filtered_ns_in_umi The number of SAM records discarded due to one or more Ns in the UMI.
+ * @param filtered_umis_to_short The number of SAM records discarded due to a shorter than expected UMI.
  */
-case class UmiGroupingMetric(reads: Long,
-                             filteredNonPf: Long,
-                             filteredPoorAlignment: Long,
-                             filteredNsInUmi: Long,
-                             filterUmisTooShort: Long) extends Metric
+case class UmiGroupingMetric(sam_records: Long,
+                             filtered_non_pf: Long,
+                             filtered_poor_alignment: Long,
+                             filtered_ns_in_umi: Long,
+                             filtered_umis_to_short: Long) extends Metric
 
 /** The strategies implemented by [[GroupReadsByUmi]] to identify reads from the same source molecule.*/
 sealed trait Strategy extends EnumEntry {
@@ -758,27 +758,25 @@ class GroupReadsByUmi
         Metric.write(p, ms)
     }
 
-  // Write out UMI grouping metrics
-  this.groupingMetrics match {
-    case None    => ()
-    case Some(p) =>
-      val groupingMetrics = UmiGroupingMetric(
-        reads                 = kept,
-        filteredNonPf         = filteredNonPf,
-        filteredPoorAlignment = filteredPoorAlignment,
-        filteredNsInUmi       = filteredNsInUmi,
-        filterUmisTooShort    = filterUmisTooShort,
-      )
-      Metric.write(p, groupingMetrics)
+    // Write out UMI grouping metrics
+    this.groupingMetrics.foreach { path =>
+        val groupingMetrics = UmiGroupingMetric(
+          sam_records             = kept,
+          filtered_non_pf         = filteredNonPf,
+          filtered_poor_alignment = filteredPoorAlignment,
+          filtered_ns_in_umi      = filteredNsInUmi,
+          filtered_umis_to_short  = filterUmisTooShort,
+        )
+      Metric.write(path, groupingMetrics)
     }
   }
 
   private def logStats(): Unit = {
-    logger.info(f"Accepted $kept%,d reads for grouping.")
-    if (filteredNonPf > 0) logger.info(f"Filtered out $filteredNonPf%,d non-PF reads.")
-    logger.info(f"Filtered out $filteredPoorAlignment%,d reads due to mapping issues.")
-    logger.info(f"Filtered out $filteredNsInUmi%,d reads that contained one or more Ns in their UMIs.")
-    this.minUmiLength.foreach { _ => logger.info(f"Filtered out $filterUmisTooShort%,d reads that contained UMIs that were too short.") }
+    logger.info(f"Accepted $kept%,d SAM records for grouping.")
+    if (filteredNonPf > 0) logger.info(f"Filtered out $filteredNonPf%,d non-PF SAM records.")
+    logger.info(f"Filtered out $filteredPoorAlignment%,d SAM records due to mapping issues.")
+    logger.info(f"Filtered out $filteredNsInUmi%,d SAM records that contained one or more Ns in their UMIs.")
+    this.minUmiLength.foreach { _ => logger.info(f"Filtered out $filterUmisTooShort%,d SAM records that contained UMIs that were too short.") }
   }
 
   /** Consumes the next group of templates with all matching end positions and returns them. */