From 85f969187cfca7ea03ca9f3a0d7276ede0702bb7 Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Mon, 1 Jul 2024 15:54:03 -0700
Subject: [PATCH] feat: add isConsensus method

---
 .../com/fulcrumgenomics/bam/api/SamRecord.scala    |  5 +++++
 .../fulcrumgenomics/bam/api/SamRecordTest.scala    | 14 ++++++++++++++
 2 files changed, 19 insertions(+)

diff --git a/src/main/scala/com/fulcrumgenomics/bam/api/SamRecord.scala b/src/main/scala/com/fulcrumgenomics/bam/api/SamRecord.scala
index cf05b54c6..40fce0b64 100644
--- a/src/main/scala/com/fulcrumgenomics/bam/api/SamRecord.scala
+++ b/src/main/scala/com/fulcrumgenomics/bam/api/SamRecord.scala
@@ -27,6 +27,7 @@ package com.fulcrumgenomics.bam.api
 
 import com.fulcrumgenomics.FgBioDef._
 import com.fulcrumgenomics.alignment.Cigar
+import com.fulcrumgenomics.umi.ConsensusTags.PerRead.AllPerReadTags
 import htsjdk.samtools
 import htsjdk.samtools.SamPairUtil.PairOrientation
 import htsjdk.samtools._
@@ -269,6 +270,10 @@ trait SamRecord {
       SamPairUtil.getPairOrientation(this) == PairOrientation.FR
   }
 
+  def isConsensus: Boolean = {
+    AllPerReadTags.exists(this.contains)
+  }
+
   /** Clone method that does a "reasonably deep" clone. The bases and quals are cloned as is the attributes map,
     * though not the values in the attributes map. */
   override def clone(): SamRecord = {
diff --git a/src/test/scala/com/fulcrumgenomics/bam/api/SamRecordTest.scala b/src/test/scala/com/fulcrumgenomics/bam/api/SamRecordTest.scala
index 38251e0c4..82f34e940 100644
--- a/src/test/scala/com/fulcrumgenomics/bam/api/SamRecordTest.scala
+++ b/src/test/scala/com/fulcrumgenomics/bam/api/SamRecordTest.scala
@@ -27,6 +27,7 @@ package com.fulcrumgenomics.bam.api
 import com.fulcrumgenomics.alignment.Cigar
 import com.fulcrumgenomics.testing.SamBuilder.{Minus, Plus}
 import com.fulcrumgenomics.testing.{SamBuilder, UnitSpec}
+import com.fulcrumgenomics.umi.ConsensusTags.PerRead.AllPerReadTags
 import htsjdk.samtools.TextCigarCodec
 import org.scalatest.OptionValues
 
@@ -289,4 +290,17 @@ class SamRecordTest extends UnitSpec with OptionValues {
     rec1.matesOverlap shouldBe None // Mate's start is not enclosed by rec, and mate's end cannot be determined
     rec2.matesOverlap.value shouldBe true // Mate's start is enclosed by rec, regardless of where mate end is
   }
+
+  "SamRecord.isConsensus" 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(_.isConsensus) shouldBe false
+    builder.addPair(start1=100, start2=100, unmapped2=true).exists(_.isConsensus) shouldBe false
+  }
+
+  it should "return true for reads with consensus tags" in {
+    val builder = new SamBuilder(sort=Some(SamOrder.Coordinate), readLength=10, baseQuality=20)
+    AllPerReadTags.forall(
+      tag => builder.addFrag(start=10, attrs=Map(tag -> 123)).exists(_.isConsensus)
+    ) shouldBe true
+  }
 }