Improvements and refactoring of Nucleotide.java

broadinstitute · Jun 1, 2018 · ec7029d · ec7029d
1 parent 3189612
commit ec7029d
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Showing 7 changed files with 566 additions and 82 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/CollectAllelicCounts.java b/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);
     }
 }
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/PreprocessIntervals.java b/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);
             }
         }

diff --git a/...roadinstitute/hellbender/tools/copynumber/formats/collections/AllelicCountCollection.java b/...roadinstitute/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);
     };