Added a slightly more helpful error message to the reads filter (#7947)

* added a summary line to the counting reads filter with totals.
broadinstitute · Dec 23, 2022 · 640d921 · 640d921
1 parent 6932ae5
commit 640d921
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Showing 2 changed files with 14 additions and 9 deletions.
diff --git 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;
+        protected 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();
         }

diff --git a/src/test/java/org/broadinstitute/hellbender/engine/filters/CountingReadFilterUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/filters/CountingReadFilterUnitTest.java
@@ -329,34 +329,37 @@ public Object[][] testAndFilterSummaryLineDataProvider() {
         final CountingReadFilter secondOfPair2 = new CountingReadFilter(ReadFilterLibrary.SECOND_OF_PAIR);
         secondOfPair2.filteredCount = 2;
 
-        final CountingReadFilter firstOfPair1AndSecondOfPair2 = firstOfPair1.and(secondOfPair2);
+        final CountingReadFilter.CountingAndReadFilter firstOfPair1AndSecondOfPair2 = (CountingReadFilter.CountingAndReadFilter)firstOfPair1.and(secondOfPair2);
         firstOfPair1AndSecondOfPair2.filteredCount = 3;
+        firstOfPair1AndSecondOfPair2.totalCount = 3;
         final String andWithCountsAbove0 = "1 read(s) filtered by: FirstOfPairReadFilter \n"
                 + "2 read(s) filtered by: SecondOfPairReadFilter \n"
-                + "3 total reads filtered";
+                + "3 total reads filtered out of 3 reads processed";
 
-        final CountingReadFilter firstOfPair1AndMappingQuality0 = firstOfPair1.and(mappingQuality0);
+        final CountingReadFilter.CountingAndReadFilter  firstOfPair1AndMappingQuality0 = (CountingReadFilter.CountingAndReadFilter)firstOfPair1.and(mappingQuality0);
         firstOfPair1AndMappingQuality0.filteredCount = 1;
+        firstOfPair1AndMappingQuality0.totalCount = 3;
         final String andWith1CountAbove0 = "1 read(s) filtered by: FirstOfPairReadFilter \n"
                 + "0 read(s) filtered by: MappingQualityAvailableReadFilter \n"
-                + "1 total reads filtered";
+                + "1 total reads filtered out of 3 reads processed";
 
-        final CountingReadFilter mappingQuality0AndGoodCigar0 = mappingQuality0.and(goodCigar0);
+        final CountingReadFilter.CountingAndReadFilter  mappingQuality0AndGoodCigar0 = (CountingReadFilter.CountingAndReadFilter)mappingQuality0.and(goodCigar0);
         mappingQuality0AndGoodCigar0.filteredCount = 0;
         final String andWithBoth0Counts = "0 read(s) filtered by: MappingQualityAvailableReadFilter \n"
                 + "0 read(s) filtered by: GoodCigarReadFilter \n"
-                + "0 total reads filtered";
+                + "0 total reads filtered out of 0 reads processed";
 
 
         final CountingReadFilter firstOfPair1AndMappingQuality0AndGoodCigar0 = firstOfPair1AndMappingQuality0.and(goodCigar0);
         firstOfPair1AndMappingQuality0AndGoodCigar0.filteredCount = 1;
-        final CountingReadFilter firstOfPair1AndMappingQuality0AndGoodCigar0AndSecondOfPair2 = firstOfPair1AndMappingQuality0AndGoodCigar0.and(secondOfPair2);
+        final CountingReadFilter.CountingAndReadFilter firstOfPair1AndMappingQuality0AndGoodCigar0AndSecondOfPair2 = (CountingReadFilter.CountingAndReadFilter)firstOfPair1AndMappingQuality0AndGoodCigar0.and(secondOfPair2);
         firstOfPair1AndMappingQuality0AndGoodCigar0AndSecondOfPair2.filteredCount = 3;
+        firstOfPair1AndMappingQuality0AndGoodCigar0AndSecondOfPair2.totalCount = 5;
         final String multiAndWithMixCounts = "1 read(s) filtered by: FirstOfPairReadFilter \n"
                 + "0 read(s) filtered by: MappingQualityAvailableReadFilter \n"
                 + "0 read(s) filtered by: GoodCigarReadFilter \n"
                 + "2 read(s) filtered by: SecondOfPairReadFilter \n"
-                + "3 total reads filtered";
+                + "3 total reads filtered out of 5 reads processed";
 
         final CountingReadFilter firstOfPair1AndMappingQuality0AndGoodCigar0OrSecondOfPair2 = firstOfPair1AndMappingQuality0AndGoodCigar0.or(secondOfPair2);
         firstOfPair1AndMappingQuality0AndGoodCigar0OrSecondOfPair2.filteredCount = 3;