From 0b68d7e85b74d38d6f796755edbd1fbd80f9deac Mon Sep 17 00:00:00 2001
From: Nils Homer <nh13@users.noreply.github.com>
Date: Mon, 24 Jul 2023 13:57:51 -0700
Subject: [PATCH] Fix pass-QC in output FASTQ read names

See #922
---
 src/main/scala/com/fulcrumgenomics/fastq/DemuxFastqs.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/com/fulcrumgenomics/fastq/DemuxFastqs.scala b/src/main/scala/com/fulcrumgenomics/fastq/DemuxFastqs.scala
index 50815c123..a6d2bbc9c 100644
--- 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(" ")
   }
 }