From 086829bd503783f6a99338a48b158739d305fba8 Mon Sep 17 00:00:00 2001
From: Kathleen Tibbetts <ktibbett@broadinstitute.org>
Date: Thu, 15 Jun 2017 10:56:55 -0400
Subject: [PATCH] PO-8928: Don't calculate improper pair metrics on unpaired
 reads

---
 src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java b/src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
index c1cb47b72..c66762b42 100644
--- a/src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
+++ b/src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
@@ -240,7 +240,7 @@ private void collectReadData(final SAMRecord record) {
                         }
                     } else if(doRefMetrics) {
                         metrics.PF_READS_ALIGNED++;
-                        if (!record.getProperPairFlag()) metrics.PF_READS_IMPROPER_PAIRS++;
+                        if (record.getReadPairedFlag() && !record.getProperPairFlag()) metrics.PF_READS_IMPROPER_PAIRS++;
                         if (!record.getReadNegativeStrandFlag()) numPositiveStrand++;
                         if (record.getReadPairedFlag() && !record.getMateUnmappedFlag()) {
                             metrics.READS_ALIGNED_IN_PAIRS++;