Fixed flipped sign when comparing read paired flags (samtools#897)

Fixed flipped sign when comparing read paired flags
EpamLifeSciencesTeam · Jun 9, 2017 · 6383b25 · 6383b25
1 parent f0f7c9b
commit 6383b25
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Showing 2 changed files with 27 additions and 2 deletions.
diff --git a/src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java b/src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java
@@ -36,7 +36,7 @@ public class DuplicateScoringStrategy {
     public enum ScoringStrategy {
         SUM_OF_BASE_QUALITIES,
         TOTAL_MAPPED_REFERENCE_LENGTH,
-        RANDOM,
+        RANDOM
     }
 
     /** Hash used for the RANDOM scoring strategy. */
@@ -128,7 +128,7 @@ public static int compare(final SAMRecord rec1, final SAMRecord rec2, final Scor
         int cmp;
 
         // always prefer paired over non-paired
-        if (rec1.getReadPairedFlag() != rec2.getReadPairedFlag()) return rec1.getReadPairedFlag() ? 1 : -1;
+        if (rec1.getReadPairedFlag() != rec2.getReadPairedFlag()) return rec1.getReadPairedFlag() ? -1 : 1;
 
         cmp = computeDuplicateScore(rec2, scoringStrategy, assumeMateCigar) - computeDuplicateScore(rec1, scoringStrategy, assumeMateCigar);
 

diff --git a/src/test/java/htsjdk/samtools/DuplicateScoringStrategyTest.java b/src/test/java/htsjdk/samtools/DuplicateScoringStrategyTest.java
@@ -0,0 +1,25 @@
+package htsjdk.samtools;
+
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+public class DuplicateScoringStrategyTest {
+
+    @DataProvider
+    public Object [][] compareData() {
+        return new Object[][]{
+                {SAMFlag.READ_PAIRED.flag, 0, true, DuplicateScoringStrategy.ScoringStrategy.RANDOM, -1},
+                {0, SAMFlag.READ_PAIRED.flag, true, DuplicateScoringStrategy.ScoringStrategy.RANDOM, 1},
+        };
+    }
+
+    @Test(dataProvider = "compareData")
+    public static void testCompare(final int samFlag1, final int samFlag2, final boolean assumeMateCigar, final DuplicateScoringStrategy.ScoringStrategy strategy, final int expected) {
+        final SAMRecord rec1 = new SAMRecordSetBuilder().addFrag("test", 0, 1, false, false, "36M", null, 2);
+        rec1.setFlags(samFlag1);
+        final SAMRecord rec2 = new SAMRecordSetBuilder().addFrag("test", 0, 1, true, false, "36M", null, 3);
+        rec2.setFlags(samFlag2);
+        Assert.assertEquals(DuplicateScoringStrategy.compare(rec1, rec2, strategy, assumeMateCigar), expected);
+    }
+}