resolving circular classloading issue and removing uses of constants …

…in SamTagUtil

src/main/java/htsjdk/samtools/BAMRecord.java

@@ -310,7 +310,7 @@ static boolean isSentinelCigar(final Cigar cigar, final int readLength) {
      * extracts the CIGAR from the CG tag and places it into the (in memory) cigar.
      */
     private void extractCigarFromCGAttribute(final Cigar sentinelCigar) throws IllegalStateException {
-        final int[] cigarFromCG = (int[]) getAttribute(SAMTagUtil.CG);
+        final int[] cigarFromCG = (int[]) getAttribute(SAMTag.CG.getBinaryTag());
 
         if (cigarFromCG == null) return;
 
@@ -353,7 +353,7 @@ private void extractCigarFromCGAttribute(final Cigar sentinelCigar) throws Illeg
         initializeCigar(decodedCigar);
 
         // remove CG attribute.
-        setAttribute(SAMTagUtil.CG, null);
+        setAttribute(SAMTag.CG.getBinaryTag(), null);
     }
 
     /**

src/main/java/htsjdk/samtools/SAMRecord.java

@@ -869,7 +869,7 @@ protected void initializeCigar(final Cigar cigar) {
      * @throws ClassCastException if RG tag does not have a String value.
      */
     public SAMReadGroupRecord getReadGroup() {
-        final String rgId = (String)getAttribute(SAMTagUtil.RG);
+        final String rgId = (String)getAttribute(SAMTag.RG.getBinaryTag());
         if (rgId == null || getHeader() == null) {
             return null;
         } else {
@@ -2063,7 +2063,7 @@ public List<SAMValidationError> isValid(final boolean firstOnly) {
 */
         }
         // Validate the RG ID is found in header
-        final String rgId = (String)getAttribute(SAMTagUtil.RG);
+        final String rgId = (String)getAttribute(SAMTag.RG.getBinaryTag());
         if (rgId != null && getHeader() != null && getHeader().getReadGroup(rgId) == null) {
                 if (ret == null) ret = new ArrayList<>();
                 ret.add(new SAMValidationError(SAMValidationError.Type.READ_GROUP_NOT_FOUND,
@@ -2078,10 +2078,10 @@ public List<SAMValidationError> isValid(final boolean firstOnly) {
         }
         // TODO(mccowan): Is this asking "is this the primary alignment"?
         if (this.getReadLength() == 0 && !this.isSecondaryAlignment()) {
-            final Object fz = getAttribute(SAMTagUtil.FZ);
+            final Object fz = getAttribute(SAMTag.FZ.getBinaryTag());
             if (fz == null) {
-                final String cq = (String)getAttribute(SAMTagUtil.CQ);
-                final String cs = (String)getAttribute(SAMTagUtil.CS);
+                final String cq = (String)getAttribute(SAMTag.CQ.getBinaryTag());
+                final String cs = (String)getAttribute(SAMTag.CS.getBinaryTag());
                 if (cq == null || cq.isEmpty() || cs == null || cs.isEmpty()) {
                     if (ret == null) ret = new ArrayList<>();
                     ret.add(new SAMValidationError(SAMValidationError.Type.EMPTY_READ,

src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java

@@ -203,7 +203,7 @@ public void setHeader(final SAMFileHeader header) {
      */
     public void addRecord(final SAMRecord record) {
         if (record.getReadPairedFlag() && !record.getMateUnmappedFlag() &&
-                null == record.getAttribute(SAMTagUtil.MC)) {
+                null == record.getAttribute(SAMTag.MC.getBinaryTag())) {
             throw new SAMException("Mate Cigar tag (MC) not found in: " + record.getReadName());
         }
         this.records.add(record);

src/main/java/htsjdk/samtools/SAMTag.java

@@ -105,7 +105,20 @@ public enum SAMTag {
     U2,
     UQ;
 
-    private final short shortValue = SAMTagUtil.makeBinaryTag(this.name());
+    private final short shortValue = SAMTag.makeBinaryTag(this.name());;
+
+    /**
+     * Convert from String representation of tag name to short representation.
+     *
+     * @param tag 2-character String representation of a tag name.
+     * @return Tag name packed as 2 ASCII bytes in a short.
+     */
+    static short makeBinaryTag(String tag) {
+        if (tag.length() != 2) {
+            throw new IllegalArgumentException("String tag does not have length() == 2: " + tag);
+        }
+        return (short)(tag.charAt(1) << 8 | tag.charAt(0));
+    }
 
     /**
      * Get the binary representation of this tag name.

src/main/java/htsjdk/samtools/SAMTagUtil.java

@@ -142,10 +142,7 @@ public static SAMTagUtil getSingleton() {
      * @return Tag name packed as 2 ASCII bytes in a short.
      */
     public static short makeBinaryTag(final String tag) {
-        if (tag.length() != 2) {
-            throw new IllegalArgumentException("String tag does not have length() == 2: " + tag);
-        }
-        return (short)(tag.charAt(1) << 8 | tag.charAt(0));
+        return SAMTag.makeBinaryTag(tag);
     }
 
     /**

src/main/java/htsjdk/samtools/SAMUtils.java

@@ -1127,7 +1127,7 @@ public static List<SAMRecord> getOtherCanonicalAlignments(final SAMRecord record
         if (record == null) throw new IllegalArgumentException("record is null");
         if (record.getHeader() == null) throw new IllegalArgumentException("record.getHeader() is null");
         /* extract value of SA tag */
-        final Object saValue = record.getAttribute(SAMTagUtil.SA);
+        final Object saValue = record.getAttribute(SAMTag.SA.getBinaryTag());
         if (saValue == null) return Collections.emptyList();
         if (!(saValue instanceof String)) throw new SAMException(
                 "Expected a String for attribute 'SA' but got " + saValue.getClass() + ". Record: " + record);
@@ -1220,7 +1220,7 @@ public static List<SAMRecord> getOtherCanonicalAlignments(final SAMRecord record
             /* fill NM */
             try {
                 if (!commaStrs[5].equals("*")) {
-                    otherRec.setAttribute(SAMTagUtil.NM, Integer.parseInt(commaStrs[5]));
+                    otherRec.setAttribute(SAMTag.NM.getBinaryTag(), Integer.parseInt(commaStrs[5]));
                 }
             } catch (final NumberFormatException err) {
                 throw new SAMException("bad NM in " + semiColonStr + ". Record: " + record, err);

src/main/java/htsjdk/samtools/SamFileValidator.java

@@ -409,7 +409,7 @@ private void validateTags(final SAMRecord record, final long recordNumber) {
             addError(new SAMValidationError(Type.CG_TAG_FOUND_IN_ATTRIBUTES,
                     "The CG Tag should only be used in BAM format to hold a large cigar. " +
                             "It was found containing the value: " +
-                            record.getAttribute(SAMTagUtil.CG), record.getReadName(), recordNumber));
+                            record.getAttribute(SAMTag.CG.getBinaryTag()), record.getReadName(), recordNumber));
         }
     }
 

src/main/java/htsjdk/samtools/sra/SRALazyRecord.java

@@ -27,13 +27,7 @@
 package htsjdk.samtools.sra;
 
 import gov.nih.nlm.ncbi.ngs.NGS;
-import htsjdk.samtools.SAMRecord;
-import htsjdk.samtools.SAMTagUtil;
-import htsjdk.samtools.SAMFileHeader;
-import htsjdk.samtools.Cigar;
-import htsjdk.samtools.SAMBinaryTagAndValue;
-import htsjdk.samtools.SAMUtils;
-import htsjdk.samtools.SAMValidationError;
+import htsjdk.samtools.*;
 import htsjdk.samtools.util.Log;
 import ngs.ReadCollection;
 import ngs.AlignmentIterator;
@@ -210,7 +204,7 @@ public String getAttribute(SRALazyRecord self) {
     static
     {
         lazyAttributeTags = new HashMap<Short, LazyAttribute>();
-        lazyAttributeTags.put(SAMTagUtil.RG, LazyAttribute.RG);
+        lazyAttributeTags.put(SAMTag.RG.getBinaryTag(), LazyAttribute.RG);
     }
 
     public SRALazyRecord(final SAMFileHeader header, SRAAccession accession, ReadCollection run, AlignmentIterator alignmentIterator, String readId, String alignmentId) {

src/test/java/htsjdk/samtools/SAMUtilsTest.java

@@ -204,7 +204,7 @@ public void testOtherCanonicalAlignments() {
         Assert.assertEquals(SAMUtils.getOtherCanonicalAlignments(record).size(),0);
 
 
-        record.setAttribute(SAMTagUtil.SA,
+        record.setAttribute(SAMTag.SA.getBinaryTag(),
                 "2,500,+,3S2=1X2=2S,60,1;" +
                 "1,191,-,8M2S,60,*;");
 
@@ -233,7 +233,7 @@ public void testOtherCanonicalAlignments() {
         Assert.assertEquals(other.getAlignmentStart(),500);
         Assert.assertFalse(other.getReadNegativeStrandFlag());
         Assert.assertEquals(other.getMappingQuality(), 60);
-        Assert.assertEquals(other.getAttribute(SAMTagUtil.NM),1);
+        Assert.assertEquals(other.getAttribute(SAMTag.NM.getBinaryTag()),1);
         Assert.assertEquals(other.getCigarString(),"3S2=1X2=2S");
         Assert.assertEquals(other.getInferredInsertSize(),0);
 
@@ -244,7 +244,7 @@ public void testOtherCanonicalAlignments() {
         Assert.assertEquals(other.getAlignmentStart(),191);
         Assert.assertTrue(other.getReadNegativeStrandFlag());
         Assert.assertEquals(other.getMappingQuality(), 60);
-        Assert.assertEquals(other.getAttribute(SAMTagUtil.NM),null);
+        Assert.assertEquals(other.getAttribute(SAMTag.NM.getBinaryTag()),null);
         Assert.assertEquals(other.getCigarString(),"8M2S");
         Assert.assertEquals(other.getInferredInsertSize(),-91);//100(mate) - 191(other)
     }