From c3aa60cb1c6a17c05053969454ea9ad671d397f2 Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Thu, 25 Jul 2024 08:12:28 -0700
Subject: [PATCH] docs: improve doc string accuracy

---
 .../com/fulcrumgenomics/umi/CollectDuplexSeqMetrics.scala    | 4 ++--
 src/main/scala/com/fulcrumgenomics/umi/Umis.scala            | 5 +++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/main/scala/com/fulcrumgenomics/umi/CollectDuplexSeqMetrics.scala b/src/main/scala/com/fulcrumgenomics/umi/CollectDuplexSeqMetrics.scala
index 30d807a7c..8e2faa94a 100644
--- a/src/main/scala/com/fulcrumgenomics/umi/CollectDuplexSeqMetrics.scala
+++ b/src/main/scala/com/fulcrumgenomics/umi/CollectDuplexSeqMetrics.scala
@@ -315,8 +315,8 @@ class CollectDuplexSeqMetrics
       rec =>
         val exceptionString = s"Input BAM file to CollectDuplexSeqMetrics ($input) appears to contain consensus sequences. " +
           "CollectDuplexSeqMetrics cannot run on consensus BAMs, and instead requires the UMI-grouped BAM generated " +
-          "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"
+          "by GroupReadsByUmi which is run prior to consensus calling." +
+          "\nFirst record in $input has consensus SAM tags present:\n$rec"
 
         if (Umis.isFgbioStyleConsensus(rec)) throw new IllegalArgumentException(exceptionString)
     }
diff --git a/src/main/scala/com/fulcrumgenomics/umi/Umis.scala b/src/main/scala/com/fulcrumgenomics/umi/Umis.scala
index 63cb4e3f7..ed5512567 100644
--- a/src/main/scala/com/fulcrumgenomics/umi/Umis.scala
+++ b/src/main/scala/com/fulcrumgenomics/umi/Umis.scala
@@ -129,9 +129,10 @@ object Umis {
     ch == 'A' || ch == 'C' || ch == 'G' || ch == 'T' || ch == 'N' || ch == '-'
   }
 
-  /** Tests if a record is a consensus or not
+  /** Returns True if the record appears to be a consensus read,
+   *  typically produced by fgbio's CallMolecularConsensusReads or CallDuplexConsensusReads.
    *
-   * @param rec the record to test
+   * @param rec the record to check
    * @return boolean indicating if the record is a consensus or not
    */
   def isFgbioStyleConsensus(rec: SamRecord): Boolean = {