From 413983acc8b63d0b252cdad0f88d97378fe3ad90 Mon Sep 17 00:00:00 2001
From: James <emeryj@broadinstitute.org>
Date: Fri, 15 Jul 2022 16:12:09 -0400
Subject: [PATCH] added a slightly better read filtering message

---
 .../hellbender/engine/filters/CountingReadFilter.java         | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/engine/filters/CountingReadFilter.java b/src/main/java/org/broadinstitute/hellbender/engine/filters/CountingReadFilter.java
index 51662ebeb4d..5a1026d1877 100644
--- a/src/main/java/org/broadinstitute/hellbender/engine/filters/CountingReadFilter.java
+++ b/src/main/java/org/broadinstitute/hellbender/engine/filters/CountingReadFilter.java
@@ -201,6 +201,7 @@ public void resetFilteredCount() {
     protected static final class CountingAndReadFilter extends CountingBinopReadFilter {
 
         private static final long serialVersionUID = 1L;
+        private long totalCount = 0;
 
         private CountingAndReadFilter(final CountingReadFilter lhs, final CountingReadFilter rhs) {
             super(lhs, rhs);
@@ -212,6 +213,7 @@ public boolean test(final GATKRead read) {
             if (!accept) {
                 filteredCount++;
             }
+            totalCount++;
             return accept;
         }
 
@@ -249,7 +251,7 @@ private String getSummaryLineForLevelAllAndsSimplified() {
                 }
             }
 
-            summaryLine.append(this.getFilteredCount() + " total reads filtered");
+            summaryLine.append(this.getFilteredCount() + " total reads filtered out of "+ this.totalCount+ " reads processed");
 
             return summaryLine.toString();
         }