Fix pass-QC in output FASTQ read names (#923)

* Fix pass-QC in output FASTQ read names See #922
fulcrumgenomics · Jul 28, 2023 · 6a2a964 · 6a2a964
1 parent e197ce4
commit 6a2a964
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/src/main/scala/com/fulcrumgenomics/fastq/DemuxFastqs.scala b/src/main/scala/com/fulcrumgenomics/fastq/DemuxFastqs.scala
@@ -913,7 +913,7 @@ object OutputType extends FgBioEnum[OutputType] {
   */
 case class ReadInfo(readNumber: Int, passQc: Boolean, internalControl: Boolean, sampleInfo: String, rest: Seq[String]) {
   override def toString: String = {
-    val leading = f"$readNumber:${if (passQc) "Y" else "N"}:${if (internalControl) 1 else 0}:$sampleInfo"
+    val leading = f"$readNumber:${if (passQc) "N" else "Y"}:${if (internalControl) 1 else 0}:$sampleInfo"
     if (rest.isEmpty) leading else leading + " " + rest.mkString(" ")
   }
 }

diff --git a/src/test/scala/com/fulcrumgenomics/fastq/DemuxFastqsTest.scala b/src/test/scala/com/fulcrumgenomics/fastq/DemuxFastqsTest.scala
@@ -1166,7 +1166,7 @@ class DemuxFastqsTest extends UnitSpec with OptionValues with ErrorLogLevel {
     val standards = FastqStandards()
     val rec       = baseRec.copy(pairedEnd=true, name="Instrument:RunID:FlowCellID:Lane:Tile:X:Y", comment=Some("1:N:0:SampleNumber")).withReadInfo
     val writer    = new FastqRecordWriter(output.resolve("prefix"), pairedEnd=true, fastqStandards=standards)
-    writer.add(rec).header shouldBe "Instrument:RunID:FlowCellID:Lane:Tile:X:Y:SB:MB 1:N:0:SampleNumber"
+    writer.add(rec).header shouldBe "Instrument:RunID:FlowCellID:Lane:Tile:X:Y:SB:MB 1:Y:0:SampleNumber"
   }
 
   it should "set the read name to include the sample barcode for single-end" in {
@@ -1175,7 +1175,7 @@ class DemuxFastqsTest extends UnitSpec with OptionValues with ErrorLogLevel {
     val standards = FastqStandards(includeSampleBarcodes=true)
     val rec       = baseRec.copy(pairedEnd=true, name="Instrument:RunID:FlowCellID:Lane:Tile:X:Y", comment=Some("1:N:0:SB")).withReadInfo
     val writer    = new FastqRecordWriter(output.resolve("prefix"), pairedEnd=false, fastqStandards=standards)
-    writer.add(rec).header shouldBe "Instrument:RunID:FlowCellID:Lane:Tile:X:Y 1:N:0:SB"
+    writer.add(rec).header shouldBe "Instrument:RunID:FlowCellID:Lane:Tile:X:Y 1:Y:0:SB"
   }
 
   it should "set the read name to include the sample barcode for paired end" in {
@@ -1184,7 +1184,7 @@ class DemuxFastqsTest extends UnitSpec with OptionValues with ErrorLogLevel {
     val standards = FastqStandards(includeSampleBarcodes=true)
     val rec       = baseRec.copy(pairedEnd=true, name="Instrument:RunID:FlowCellID:Lane:Tile:X:Y", comment=Some("1:Y:0:SB1+SB2"), sampleBarcode=Seq("SB1","SB2"), molecularBarcode=Seq("MB1","MB2")).withReadInfo
     val writer    = new FastqRecordWriter(output.resolve("prefix"), pairedEnd=true, fastqStandards=standards)
-    writer.add(rec).header shouldBe "Instrument:RunID:FlowCellID:Lane:Tile:X:Y 1:Y:0:SB1+SB2"
+    writer.add(rec).header shouldBe "Instrument:RunID:FlowCellID:Lane:Tile:X:Y 1:N:0:SB1+SB2"
   }
 
   "ReadInfo" should "not be built if there was no comment in the given record when following Illumina standards" in {