Change to PairOrientation stratifier and typo fix

- The PairOrientation stratifier now checks if the read is paired and returns null if it is not - fixed small typo originating from the separation of the PRs
broadinstitute · Aug 12, 2019 · 7a5c757 · 7a5c757
1 parent cde82fb
commit 7a5c757
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Showing 3 changed files with 10 additions and 5 deletions.
diff --git a/src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java b/src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java
@@ -408,7 +408,7 @@ else if (!currentLocus.withinDistanceOf(locusInfo, 0)) {
      * @param info           The SAMLocusAndReference object
      * @param operation      Classifies whether the current event is a match, insertion, or deletion
      */
-    private void addAndRecordAndOffset(final Collection<BaseErrorAggregation> aggregatorList, final SamLocusIterator.RecordAndOffset rao, final SAMLocusAndReference info, final BaseOperation operation) {
+    private void addRecordAndOffset(final Collection<BaseErrorAggregation> aggregatorList, final SamLocusIterator.RecordAndOffset rao, final SAMLocusAndReference info, final BaseOperation operation) {
         // If deletion has been processed already, skip it
         if (operation == BaseOperation.Deletion && processDeletionLocus(rao, info.getLocus()))
             return;
@@ -424,17 +424,17 @@ private void addAndRecordAndOffset(final Collection<BaseErrorAggregation> aggreg
     private void addLocusBases(final Collection<BaseErrorAggregation> aggregatorList, final SAMLocusAndReference info) {
         // Matching bases
         for (final SamLocusIterator.RecordAndOffset rao : info.getRecordAndOffsets()) {
-            addAndRecordAndOffset(aggregatorList, rao, info, BaseOperation.Match);
+            addRecordAndOffset(aggregatorList, rao, info, BaseOperation.Match);
         }
 
         // Deleted bases
         for (final SamLocusIterator.RecordAndOffset deletionRao : info.getLocus().getDeletedInRecord()) {
-            addAndRecordAndOffset(aggregatorList, deletionRao, info, BaseOperation.Deletion);
+            addRecordAndOffset(aggregatorList, deletionRao, info, BaseOperation.Deletion);
         }
 
         // Inserted bases
         for (final SamLocusIterator.RecordAndOffset insertionRao : info.getLocus().getInsertedInRecord()) {
-            addAndRecordAndOffset(aggregatorList, insertionRao, info, BaseOperation.Insertion);
+            addRecordAndOffset(aggregatorList, insertionRao, info, BaseOperation.Insertion);
         }
     }
 

diff --git a/src/main/java/picard/sam/SamErrorMetric/ReadBaseStratification.java b/src/main/java/picard/sam/SamErrorMetric/ReadBaseStratification.java
@@ -932,6 +932,11 @@ public static PairOrientation of(final SAMRecord sam) {
             final ReadOrdinality ordinality = ReadOrdinality.of(sam);
             final ReadDirection direction = ReadDirection.of(sam);
 
+            // Make sure that the read is paired
+            if (!sam.getReadPairedFlag()) {
+                return null;
+            }
+
             // if read is unmapped, read isn't mapped, or mate is unmapped, return null
             if (direction == null ||
                     sam.getReadUnmappedFlag() ||

diff --git a/src/test/java/picard/sam/SamErrorMetric/CollectSamErrorMetricsTest.java b/src/test/java/picard/sam/SamErrorMetric/CollectSamErrorMetricsTest.java
@@ -615,7 +615,7 @@ public Object[][] provideForTestIndelErrors() {
                 // insertions & deletions
                 { new String[] { "20M2I20M3D20M" }, ".indel_error_by_indel_length", new IndelErrorMetric("2", 2, 1, 2, 0, 0) },
                 { new String[] { "20M2I20M3D20M" }, ".indel_error_by_indel_length", new IndelErrorMetric("3", 0, 0, 0, 1, 3) },
-                { new String[] { "2I2D20M" },       ".indel_error_by_indel_length", new IndelErrorMetric("2", 2, 1,  2,1, 2) },
+                { new String[] { "2I2D20M" },       ".indel_error_by_indel_length", new IndelErrorMetric("2", 2, 1, 2, 1, 2) },
                 { new String[] { "2D2I20M" },       ".indel_error_by_indel_length", new IndelErrorMetric("2", 2, 1, 2, 1, 2) },
                 { new String[] { "2M2D2I" },        ".indel_error_by_indel_length", new IndelErrorMetric("2", 2, 1, 2, 1, 2) },
                 { new String[] { "20M2I2D" },       ".indel_error_by_indel_length", new IndelErrorMetric("2", 2, 1, 2, 1, 2) },