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fulcrumgenomics · Sep 1, 2023 · 172e0df · 172e0df
1 parent 645bf0d
commit 172e0df
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Showing 2 changed files with 21 additions and 11 deletions.
diff --git a/src/main/scala/com/fulcrumgenomics/fastq/FastqToBam.scala b/src/main/scala/com/fulcrumgenomics/fastq/FastqToBam.scala
@@ -92,7 +92,7 @@ class FastqToBam
   @arg(flag='s', doc="If true, queryname sort the BAM file, otherwise preserve input order.")  val sort: Boolean = false,
   @arg(flag='u', doc="Tag in which to store molecular barcodes/UMIs.")                         val umiTag: String = ConsensusTags.UmiBases,
   @arg(flag='q', doc="Tag in which to store molecular barcode/UMI qualities.")                 val umiQualTag: Option[String] = None,
-  @arg(doc="Store the sample barcode qualities in the QT Tag.")                                val storeSampleBarcodeQualities: Boolean = false,
+  @arg(flag='Q', doc="Store the sample barcode qualities in the QT Tag.")                      val storeSampleBarcodeQualities: Boolean = false,
   @arg(flag='n', doc="Extract UMI(s) from read names and prepend to UMIs from reads.")         val extractUmisFromReadNames: Boolean = false,
   @arg(          doc="Read group ID to use in the file header.")                               val readGroupId: String = "A",
   @arg(          doc="The name of the sequenced sample.")                                      val sample: String,
@@ -184,7 +184,7 @@ class FastqToBam
 
         if (sampleBarcode.nonEmpty) rec("BC") = sampleBarcode
         if (storeSampleBarcodeQualities && sampleQuals.nonEmpty) rec("QT") = sampleQuals
-        
+
         // Set the UMI on the read depending on whether we got UMIs from the read names, reads or both
         (umi, umiFromReadName) match {
           case ("",       Some(fromName)) => rec(this.umiTag) = fromName

diff --git a/src/test/scala/com/fulcrumgenomics/fastq/FastqToBamTest.scala b/src/test/scala/com/fulcrumgenomics/fastq/FastqToBamTest.scala
@@ -329,15 +329,25 @@ class FastqToBamTest extends UnitSpec {
       FastqRecord("q3:2:3:4:5:6:7", "GAACCCTCGA", "CDEFGHIJKL"),
     )
     val bam = makeTempFile("fastqToBamTest.", ".bam")
-    new FastqToBam(input = Seq(r1), output = bam, sample = "s", library = "l", readStructures = Seq(rs("3B3M3B+T")), storeSampleBarcodeQualities = true).execute()
-    val recs = readBamRecs(bam)
-    recs should have size 3
-    recs(0).apply[String]("BC") shouldBe "AAA-AAA"
-    recs(0).apply[String]("QT") shouldBe "ABC GHI"
-    recs(1).apply[String]("BC") shouldBe "TAA-AAA"
-    recs(1).apply[String]("QT") shouldBe "BCD HIJ"
-    recs(2).apply[String]("BC") shouldBe "GAA-TCG"
-    recs(2).apply[String]("QT") shouldBe "CDE IJK"
+
+    Seq(true, false).foreach { storeSampleBarcodeQualities =>
+      new FastqToBam(input = Seq(r1), output = bam, sample = "s", library = "l", readStructures = Seq(rs("3B3M3B+T")), storeSampleBarcodeQualities = storeSampleBarcodeQualities).execute()
+      val recs = readBamRecs(bam)
+      recs should have size 3
+      recs(0).apply[String]("BC") shouldBe "AAA-AAA"
+      recs(1).apply[String]("BC") shouldBe "TAA-AAA"
+      recs(2).apply[String]("BC") shouldBe "GAA-TCG"
+
+      if (storeSampleBarcodeQualities) {
+        recs(0).apply[String]("QT") shouldBe "ABC GHI"
+        recs(1).apply[String]("QT") shouldBe "BCD HIJ"
+        recs(2).apply[String]("QT") shouldBe "CDE IJK"
+      } else {
+        Range.inclusive(0, 2).foreach { index =>
+          recs(index).contains("QT") shouldBe false
+        }
+      }
+    }
   }
 
   it should "extract UMIs from read names when requested" in {