From 2c97cce4a12ce72af6d4582700437328a6fb397b Mon Sep 17 00:00:00 2001
From: meganshand <mshand@broadinstitute.org>
Date: Mon, 7 Jan 2019 14:15:15 -0500
Subject: [PATCH] IntervalKeepPairFilter now filters out single ended reads
 (#1252)

* fix an exception when seeing unpaired reads
---
 .../samtools/filter/IntervalKeepPairFilter.java |  6 +++---
 .../filter/IntervalKeepPairFilterTest.java      | 17 +++++++++++++++++
 2 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/src/main/java/htsjdk/samtools/filter/IntervalKeepPairFilter.java b/src/main/java/htsjdk/samtools/filter/IntervalKeepPairFilter.java
index c4e01aae2d..9a6d564020 100644
--- a/src/main/java/htsjdk/samtools/filter/IntervalKeepPairFilter.java
+++ b/src/main/java/htsjdk/samtools/filter/IntervalKeepPairFilter.java
@@ -58,8 +58,8 @@ public IntervalKeepPairFilter(final List<Interval> intervals) {
      * overlaps the current interval using overlap detector. If yes, return
      * false -> don't filter it out.
      *
-     * If a read is secondary or supplementary, filter read out. Use
-     * {@link IntervalFilter} if you want to keep these reads, but NOTE: the
+     * If a read is secondary, supplementary, or single ended, filter read out.
+     * Use {@link IntervalFilter} if you want to keep these reads, but NOTE: the
      * resulting bam may not be valid.
      *
      * @param record the SAMRecord to evaluate
@@ -67,7 +67,7 @@ public IntervalKeepPairFilter(final List<Interval> intervals) {
      */
     @Override
     public boolean filterOut(final SAMRecord record) {
-        if (record.isSecondaryOrSupplementary()) {
+        if (record.isSecondaryOrSupplementary() || !record.getReadPairedFlag()) {
            return true;
         }
 
diff --git a/src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java b/src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java
index 59e60d03b9..187313d0a0 100644
--- a/src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java
+++ b/src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java
@@ -48,6 +48,8 @@ public void setUp() {
         builder.addFrag("mapped_pair_chr1", 0, 1, false, false, "151M", null, -1, true, false);
         // Supplementary alignment are never kept by the interval filter.
         builder.addFrag("mapped_pair_chr1", 0, 1, false, false, "151M", null, -1, false, true);
+        // Single ended read should never be kept by the interval filter.
+        builder.addFrag("single_ended", 0, 1, false);
     }
 
     @Test(dataProvider = "testData")
@@ -96,6 +98,21 @@ public void testNotPrimaryReads() {
         Assert.assertFalse(notPrimary);
     }
 
+    @Test
+    public void testSingleEndedReads() {
+        final List<Interval> intervalList = new ArrayList<>();
+        final Interval interval1 = new Interval("chr1", 1, 999);
+        intervalList.add(interval1);
+
+        final IntervalKeepPairFilter filter = new IntervalKeepPairFilter(intervalList);
+
+        boolean singleEnded = StreamSupport.stream(builder.spliterator(), false)
+                .filter(rec -> !filter.filterOut(rec))
+                .anyMatch(rec -> rec.getReadName().equals("single_ended"));
+
+        Assert.assertFalse(singleEnded);
+    }
+
     @DataProvider(name = "testData")
     private Object[][] testData() {
         Interval interval = new Interval("chr1", 1, 999);