Improvements and refactoring of Nucleotide.java (#4846)

Various improvements and refactoring of Nucleotide.java:

* More succinct constant initialization making it easer to read what nucleotides are covered by ambiguous codes.
* Added comprehensive list of long form name constants.
* valueOf/name/toString -> decode/encodeAs??? 
* Additional metods to obtain the complement, transition and trasversion nucleotides.

src/main/java/org/broadinstitute/hellbender/tools/copynumber/CollectAllelicCounts.java

@@ -149,6 +149,6 @@ public Object onTraversalSuccess() {
     @Override
     public void apply(AlignmentContext alignmentContext, ReferenceContext referenceContext, FeatureContext featureContext) {
         final byte refAsByte = referenceContext.getBase();
-        allelicCountCollector.collectAtLocus(Nucleotide.valueOf(refAsByte), alignmentContext.getBasePileup(), alignmentContext.getLocation(), minimumBaseQuality);
+        allelicCountCollector.collectAtLocus(Nucleotide.decode(refAsByte), alignmentContext.getBasePileup(), alignmentContext.getLocation(), minimumBaseQuality);
     }
 }

src/main/java/org/broadinstitute/hellbender/tools/copynumber/PreprocessIntervals.java

@@ -202,7 +202,7 @@ private static IntervalList generateBins(final IntervalList preparedIntervalList
     private static IntervalList filterBinsContainingOnlyNs(final IntervalList unfilteredBins, final ReferenceDataSource reference) {
         final IntervalList bins = new IntervalList(reference.getSequenceDictionary());
         for (final Interval unfilteredBin : unfilteredBins) {
-            if (!Utils.stream(reference.query(new SimpleInterval(unfilteredBin))).allMatch(b -> b == Nucleotide.N.toBase())) {
+            if (!Utils.stream(reference.query(new SimpleInterval(unfilteredBin))).allMatch(b -> Nucleotide.decode(b) == Nucleotide.N)) {
                 bins.add(unfilteredBin);
             }
         }

src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/collections/AllelicCountCollection.java

@@ -40,8 +40,8 @@ enum AllelicCountTableColumn {
         final int position = dataLine.getInt(AllelicCountTableColumn.POSITION);
         final int refReadCount = dataLine.getInt(AllelicCountTableColumn.REF_COUNT);
         final int altReadCount = dataLine.getInt(AllelicCountTableColumn.ALT_COUNT);
-        final Nucleotide refNucleotide = Nucleotide.valueOf(dataLine.get(AllelicCountTableColumn.REF_NUCLEOTIDE.name()).getBytes()[0]);
-        final Nucleotide altNucleotide = Nucleotide.valueOf(dataLine.get(AllelicCountTableColumn.ALT_NUCLEOTIDE.name()).getBytes()[0]);
+        final Nucleotide refNucleotide = Nucleotide.decode(dataLine.get(AllelicCountTableColumn.REF_NUCLEOTIDE.name()).charAt(0));
+        final Nucleotide altNucleotide = Nucleotide.decode(dataLine.get(AllelicCountTableColumn.ALT_NUCLEOTIDE.name()).charAt(0));
         final SimpleInterval interval = new SimpleInterval(contig, position, position);
         return new AllelicCount(interval, refReadCount, altReadCount, refNucleotide, altNucleotide);
     };

src/main/java/org/broadinstitute/hellbender/tools/walkers/readorientation/AltSiteRecord.java

@@ -29,7 +29,7 @@ public class AltSiteRecord {
 
     public AltSiteRecord(final String referenceContext, final int refCount, final int altCount,
                          final int refF1R2, final int altF1R2, final Nucleotide altAllele){
-        Utils.validateArg(Nucleotide.REGULAR_BASES.contains(altAllele), "altAllele must be one of {A,C,G,T} but got " + altAllele);
+        Utils.validateArg(altAllele != null && altAllele.isStandard(), "altAllele must be one of {A,C,G,T} but got " + altAllele);
 
         this.referenceContext = referenceContext;
         this.refCount = refCount;
@@ -63,7 +63,7 @@ public AltSiteRecord(final String referenceContext, final int refCount, final in
     public AltSiteRecord getReverseComplementOfRecord(){
         Utils.validate(!F1R2FilterConstants.CANONICAL_KMERS.contains(referenceContext), "for consistency, don't make the " +
                         "revcomp record of a canonical reference context");
-        final Nucleotide revCompOfAlt = Nucleotide.complement(altAllele.toBase());
+        final Nucleotide revCompOfAlt = altAllele.complement();
         final int newRefF1R2 = refCount - refF1R2;
         final int newAltF1R2 = altCount - altF1R2;
         return new AltSiteRecord(SequenceUtil.reverseComplement(referenceContext), refCount, altCount, newRefF1R2,

src/main/java/org/broadinstitute/hellbender/tools/walkers/readorientation/CollectF1R2Counts.java

@@ -154,14 +154,14 @@ public void apply(final AlignmentContext alignmentContext, final ReferenceContex
         }
 
         // If we got here, we have an alt site with a single alt base
-        final Nucleotide altBase = Nucleotide.valueOf(BaseUtils.baseIndexToSimpleBase(altBaseIndex));
+        final Nucleotide altBase = Nucleotide.decode(BaseUtils.baseIndexToSimpleBase(altBaseIndex));
 
         final int refCount = baseCounts[refBase.ordinal()];
         final int altCount = baseCounts[altBaseIndex];
         Utils.validate(altCount > 0, "We must have a nonzero alt read but got " + altCount);
 
-        final int refF1R2 = pileup.getNumberOfElements(pe -> Nucleotide.valueOf(pe.getBase()) == refBase && ReadUtils.isF1R2(pe.getRead()));
-        final int altF1R2 = pileup.getNumberOfElements(pe -> Nucleotide.valueOf(pe.getBase()) == altBase && ReadUtils.isF1R2(pe.getRead()));
+        final int refF1R2 = pileup.getNumberOfElements(pe -> Nucleotide.decode(pe.getBase()) == refBase && ReadUtils.isF1R2(pe.getRead()));
+        final int altF1R2 = pileup.getNumberOfElements(pe -> Nucleotide.decode(pe.getBase()) == altBase && ReadUtils.isF1R2(pe.getRead()));
 
         if (altCount == 1) {
             final ReadOrientation type = altF1R2 == 1 ? F1R2 : F2R1;

src/main/java/org/broadinstitute/hellbender/tools/walkers/readorientation/DepthOneHistograms.java

@@ -24,9 +24,9 @@ public DepthOneHistograms(final int maxDepth) {
 
         // Initialize, for each reference context, the (Alt Allele, Artifact Type) -> Histogram map
         F1R2FilterConstants.ALL_KMERS.forEach(context -> {
-            map.put(context, new HashMap<>((Nucleotide.REGULAR_BASES.size() - 1) * ReadOrientation.SIZE));
+            map.put(context, new HashMap<>((Nucleotide.STANDARD_BASES.size() - 1) * ReadOrientation.SIZE));
 
-            for (Nucleotide altAllele : Nucleotide.REGULAR_BASES) {
+            for (Nucleotide altAllele : Nucleotide.STANDARD_BASES) {
                 // Skip e.g. AGT -> AGT because G is not an alt allele
 
                 if (altAllele == F1R2FilterUtils.getMiddleBase(context)) {

src/main/java/org/broadinstitute/hellbender/tools/walkers/readorientation/F1R2FilterConstants.java

@@ -40,7 +40,7 @@ public class F1R2FilterConstants {
     // We combine all sites of depths above this value in the last bin of the histogram
     static final int DEFAULT_MAX_DEPTH = 200;
 
-    static final int numAltHistogramsPerContext = (Nucleotide.REGULAR_BASES.size() - 1) * (ReadOrientation.values().length);
+    static final int numAltHistogramsPerContext = (Nucleotide.STANDARD_BASES.size() - 1) * (ReadOrientation.values().length);
 
     public static Integer[] getEmptyBins(final int maxDepth){
         return IntStream.rangeClosed(1, maxDepth).boxed().toArray( Integer[]::new );

src/main/java/org/broadinstitute/hellbender/tools/walkers/readorientation/LearnReadOrientationModel.java

@@ -180,7 +180,7 @@ public static List<Histogram<Integer>> combineAltDepthOneHistogramWithRC(final L
 
         final List<Histogram<Integer>> combinedHistograms = new ArrayList<>(F1R2FilterConstants.numAltHistogramsPerContext);
 
-        for (Nucleotide altAllele : Nucleotide.REGULAR_BASES){
+        for (Nucleotide altAllele : Nucleotide.STANDARD_BASES){
             // Skip when the alt base is the ref base, which doesn't make sense because this is a histogram of alt sites
             if (altAllele == F1R2FilterUtils.getMiddleBase(refContext)){
                 continue;

src/main/java/org/broadinstitute/hellbender/tools/walkers/readorientation/LearnReadOrientationModelEngine.java

@@ -197,7 +197,7 @@ private void takeEstep(final double[] artifactPriors) {
         // Compute the responsibilities of alt sites with depth=1
         for (int i = 0; i < maxDepth; i++){
             final int depth = i+1;
-            for (Nucleotide altAllele : Nucleotide.REGULAR_BASES){
+            for (Nucleotide altAllele : Nucleotide.STANDARD_BASES){
                 for (ReadOrientation orientation : ReadOrientation.values()){
                     if (altAllele == refAllele){
                         continue;