Fixes edge case where soft-cliped portion of a read ends up at a nega…

src/main/java/picard/sam/AbstractAlignmentMerger.java

@@ -791,7 +791,7 @@ protected static void clipForOverlappingReads(final SAMRecord read1, final SAMRe
         }
     }
 
-    private static int getReadPositionAtReferencePositionIgnoreSoftClips(final SAMRecord rec, final int pos) {
+    static int getReadPositionAtReferencePositionIgnoreSoftClips(final SAMRecord rec, final int pos) {
         final int readPosition;
         final Cigar oldCigar = rec.getCigar();
         final int oldStart = rec.getAlignmentStart();
@@ -819,10 +819,12 @@ private static int getReadPositionAtReferencePositionIgnoreSoftClips(final SAMRe
 
         // Temporarily use the newCigar that has SOFT_CLIPs replaced with MATCH_OR_MISMATCH to get read position at reference, but ignore existence of soft-clips
         rec.setCigar(newCigar);
-        readPosition = SAMRecord.getReadPositionAtReferencePosition(rec, pos, false);
+        // Since the read effectively got shifted forward by turning the clips into matches, the query position needs
+        // also to be moved forward bye posShift so that it's still querying the same base.
+        readPosition = SAMRecord.getReadPositionAtReferencePosition(rec, pos + posShift, false);
         rec.setCigar(oldCigar);
-        // instead of setting back the position of the read by posShift, which could create a negative start position, we add posShift the final position in the read.
-        return readPosition + posShift;
+
+        return readPosition;
     }
 
     private static void clip3PrimeEndOfRead(final SAMRecord rec, final int clipFrom, final boolean useHardClipping) {

src/test/java/picard/sam/AbstractAlignmentMergerTest.java

@@ -250,5 +250,29 @@ private static File newTempSamFile(final String filename) throws IOException {
         file.deleteOnExit();
         return file;
     }
+    @DataProvider(name = "readPositionIgnoringSoftClips")
+    public Object[][] readPositionIgnoringSoftClips() {
+        return new Object[][] {
+                {"26S58M62S", 3688, 3827, 0}, // This is from the read that made us aware of a bug
+                {"26S58M62S", 3688, 3665, 4},
+                {"26S58M62S", 3688, 3660, 0}, // Before soft clip
+                {"10S100M2S", 5, 10, 16},
+                {"10S100M2S", 5, 3, 9},
+                {"10S100M2S", 10, 12, 13},
+                {"10S100M2S", 5, 107, 0}
+        };
+    }
+    @Test(dataProvider = "readPositionIgnoringSoftClips")
+    public void testGetReadPositionIgnoringSoftClips(final String cigarString, final int startPosition, final int queryPosition, final int expectedReadPosititon) {
+        final SAMFileHeader newHeader = SAMRecordSetBuilder.makeDefaultHeader(SAMFileHeader.SortOrder.queryname, 100000,false);
+        final SAMRecord rec = new SAMRecord(newHeader);
+
+        rec.setCigarString(cigarString);
+        rec.setAlignmentStart(startPosition);
+
+        final int readPosition = AbstractAlignmentMerger.getReadPositionAtReferencePositionIgnoreSoftClips(rec, queryPosition);
+
+        Assert.assertEquals(readPosition, expectedReadPosititon);
+    }
 }