Update htsjdk (#1482)

* update htsjdk 2.21.2 -> 2.21.3
* update code that changed because of clipping improvements

build.gradle

@@ -65,7 +65,7 @@ def ensureBuildPrerequisites(rbuildPrerequisitesMessage) {
 
 ensureBuildPrerequisites(buildPrerequisitesMessage)
 
-final htsjdkVersion = System.getProperty('htsjdk.version', '2.21.2')
+final htsjdkVersion = System.getProperty('htsjdk.version', '2.21.3')
 final googleNio = 'com.google.cloud:google-cloud-nio:0.107.0-alpha:shaded'
 
 // Get the jdk files we need to run javaDoc. We need to use these during compile, testCompile,

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

@@ -773,14 +773,12 @@ protected static void clipForOverlappingReads(final SAMRecord read1, final SAMRe
                         final int clipped = lengthOfSoftClipping(elems.iterator());
                         final int clipFrom = pos.getReadLength() - posDiff - clipped + 1;
                         CigarUtil.softClip3PrimeEndOfRead(pos, Math.min(pos.getReadLength(), clipFrom));
-                        removeNmMdAndUqTags(pos); // these tags are now invalid!
                     }
 
                     if (negDiff > 0) {
                         final int clipped = lengthOfSoftClipping(neg.getCigar().getCigarElements().iterator());
                         final int clipFrom = neg.getReadLength() - negDiff - clipped + 1;
                         CigarUtil.softClip3PrimeEndOfRead(neg, Math.min(neg.getReadLength(), clipFrom));
-                        removeNmMdAndUqTags(neg); // these tags are now invalid!
                     }
                 }
             }
@@ -925,7 +923,6 @@ protected void updateCigarForTrimmedOrClippedBases(final SAMRecord rec, final SA
         // If the adapter sequence is marked and clipAdapter is true, clip it
         if (this.clipAdapters && rec.getAttribute(ReservedTagConstants.XT) != null) {
             CigarUtil.softClip3PrimeEndOfRead(rec, rec.getIntegerAttribute(ReservedTagConstants.XT));
-            removeNmMdAndUqTags(rec); // these tags are now invalid!
         }
     }
 
@@ -989,15 +986,4 @@ public void setIncludeSecondaryAlignments(final boolean includeSecondaryAlignmen
     public void close() {
         CloserUtil.close(this.refSeq);
     }
-
-
-    /** Removes the NM, MD, and UQ tags.  This is useful if we modify the read and are not able to recompute these tags,
-     * for example when no reference is available.
-     * @param rec the record to modify.
-     */
-    private static void removeNmMdAndUqTags(final SAMRecord rec) {
-        rec.setAttribute(SAMTag.NM.name(), null);
-        rec.setAttribute(SAMTag.MD.name(), null);
-        rec.setAttribute(SAMTag.UQ.name(), null);
-    }
 }

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

@@ -70,9 +70,9 @@ public class AbstractAlignmentMergerTest extends CommandLineProgramTest {
         final SAMRecord r2 = recs.get(1);
         AbstractAlignmentMerger.clipForOverlappingReads(r1, r2);
         Assert.assertEquals(r1.getAlignmentStart(), 100);
-        Assert.assertEquals(r1.getCigarString(), "100M20S"); // Should ideally be 100M20S5H
+        Assert.assertEquals(r1.getCigarString(), "100M20S5H");
         Assert.assertEquals(r2.getAlignmentStart(), 100);
-        Assert.assertEquals(r2.getCigarString(), "20S100M"); // Should ideally be 5H20S100M
+        Assert.assertEquals(r2.getCigarString(), "5H20S100M");
     }