Edits to work with the latest htsjdk release:

* TextCigarCodec.decode() is now static, and the getSingleton() method is gone
 * MergingSamRecordIterator now wants a Collection<SamReader> rather than Collection<SAMFileReader> in the constructor
 * SeekableBufferedStream now correctly reads the requested number of bytes, removed workaround in GATKBAMIndex

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java

@@ -269,8 +269,8 @@ public class LDMergerUnitTest extends BaseTest {
 
     @Test(dataProvider = "R2MergerData")
     public void testR2Merger(final String refS, final String hapS, int nEvents, final String cigar, final String expectedMergedRef, final String expectedMergedAlt, final double r2, final boolean expectMerge) {
-        final Haplotype ref = new Haplotype(refS.getBytes(), true, 0, TextCigarCodec.getSingleton().decode(refS.length() + "M"));
+        final Haplotype ref = new Haplotype(refS.getBytes(), true, 0, TextCigarCodec.decode(refS.length() + "M"));
-        final Haplotype hap = new Haplotype(hapS.getBytes(), false, 0, TextCigarCodec.getSingleton().decode(cigar));
+        final Haplotype hap = new Haplotype(hapS.getBytes(), false, 0, TextCigarCodec.decode(cigar));
         final GenomeLoc loc = new UnvalidatingGenomeLoc("1", 0, 1, ref.length());
 
         final List<Haplotype> haplotypes = Arrays.asList(ref, hap);
@@ -294,9 +294,9 @@ public class LDMergerUnitTest extends BaseTest {
         final String refS = "ACGT";
         final String hapS = "CCGA";
         final String cigar = "4M";
-        final Haplotype ref = new Haplotype(refS.getBytes(), true, 0, TextCigarCodec.getSingleton().decode(refS.length() + "M"));
+        final Haplotype ref = new Haplotype(refS.getBytes(), true, 0, TextCigarCodec.decode(refS.length() + "M"));
-        final Haplotype hap1 = new Haplotype(hapS.getBytes(), false, 0, TextCigarCodec.getSingleton().decode(cigar));
+        final Haplotype hap1 = new Haplotype(hapS.getBytes(), false, 0, TextCigarCodec.decode(cigar));
-        final Haplotype hap2 = new Haplotype("ACGA".getBytes(), false, 0, TextCigarCodec.getSingleton().decode(cigar));
+        final Haplotype hap2 = new Haplotype("ACGA".getBytes(), false, 0, TextCigarCodec.decode(cigar));
         final GenomeLoc loc = new UnvalidatingGenomeLoc("1", 0, 1, ref.length());
 
         final List<Haplotype> haplotypes = Arrays.asList(ref, hap1, hap2);
@@ -321,12 +321,12 @@ public class LDMergerUnitTest extends BaseTest {
         final String refS = "ACGT";
         final String hapS = "TCGA";
         final String cigar = "4M";
-        final Haplotype ref = new Haplotype(refS.getBytes(), true, 0, TextCigarCodec.getSingleton().decode(refS.length() + "M"));
+        final Haplotype ref = new Haplotype(refS.getBytes(), true, 0, TextCigarCodec.decode(refS.length() + "M"));
-        final Haplotype hap1 = new Haplotype(hapS.getBytes(), false, 0, TextCigarCodec.getSingleton().decode(cigar));
+        final Haplotype hap1 = new Haplotype(hapS.getBytes(), false, 0, TextCigarCodec.decode(cigar));
 
         final GenomeLoc loc = new UnvalidatingGenomeLoc("1", 0, 1, ref.length());
         for (final String hap2S : Arrays.asList("GCGA", "TCGG")) {
-            final Haplotype hap2 = new Haplotype(hap2S.getBytes(), false, 0, TextCigarCodec.getSingleton().decode(cigar));
+            final Haplotype hap2 = new Haplotype(hap2S.getBytes(), false, 0, TextCigarCodec.decode(cigar));
 
             final List<Haplotype> haplotypes = Arrays.asList(ref, hap1, hap2);
             final TreeSet<Integer> vcStarts = EventMap.buildEventMapsForHaplotypes(haplotypes, ref.getBases(), loc, false);

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java

@@ -452,7 +452,7 @@ public class KBestHaplotypeFinderUnitTest extends BaseTest {
         Cigar expected = new Cigar();
         expected.add(new CigarElement(padSize, CigarOperator.M));
         if ( ! prefix.equals("") ) expected.add(new CigarElement(prefix.length(), CigarOperator.M));
-        for ( final CigarElement elt : TextCigarCodec.getSingleton().decode(midCigar).getCigarElements() ) expected.add(elt);
+        for ( final CigarElement elt : TextCigarCodec.decode(midCigar).getCigarElements() ) expected.add(elt);
         if ( ! end.equals("") ) expected.add(new CigarElement(end.length(), CigarOperator.M));
         expected.add(new CigarElement(padSize, CigarOperator.M));
         expected = AlignmentUtils.consolidateCigar(expected);
@@ -513,7 +513,7 @@ public class KBestHaplotypeFinderUnitTest extends BaseTest {
     public void testLeftAlignCigarSequentiallyAdjacentID() {
         final String ref = "GTCTCTCTCTCTCTCTCTATATATATATATATATTT";
         final String hap = "GTCTCTCTCTCTCTCTCTCTCTATATATATATATTT";
-        final Cigar originalCigar = TextCigarCodec.getSingleton().decode("18M4I12M4D2M");
+        final Cigar originalCigar = TextCigarCodec.decode("18M4I12M4D2M");
 
         final Cigar result = CigarUtils.leftAlignCigarSequentially(originalCigar, ref.getBytes(), hap.getBytes(), 0, 0);
         logger.warn("Result is " + result);

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java

@@ -82,7 +82,7 @@ public class HaplotypeBAMWriterUnitTest extends BaseTest {
 
     private Haplotype makeHaplotype(final String bases, final String cigar) {
         final Haplotype hap = new Haplotype(bases.getBytes());
-        hap.setCigar(TextCigarCodec.getSingleton().decode(cigar));
+        hap.setCigar(TextCigarCodec.decode(cigar));
         return hap;
     }
 
@@ -160,7 +160,7 @@ public class HaplotypeBAMWriterUnitTest extends BaseTest {
             final String badCigar = "31M6D211M";
             final String goodCigar = "28M6D214M";
             final Haplotype badHap = new Haplotype(hap.getBytes());
-            badHap.setCigar(TextCigarCodec.getSingleton().decode(hapCigar));
+            badHap.setCigar(TextCigarCodec.decode(hapCigar));
             badHap.setAlignmentStartHapwrtRef(hapStart);
 
             final int expectedPos = 10130740;
@@ -179,7 +179,7 @@ public class HaplotypeBAMWriterUnitTest extends BaseTest {
         if ( expectedReadCigar == null ) {
             Assert.assertNull(AlignmentUtils.createReadAlignedToRef(read, haplotype, haplotype, refStart, true));
         } else {
-            final Cigar expectedCigar = TextCigarCodec.getSingleton().decode(expectedReadCigar);
+            final Cigar expectedCigar = TextCigarCodec.decode(expectedReadCigar);
             final GATKSAMRecord alignedRead = AlignmentUtils.createReadAlignedToRef(read, haplotype, haplotype, refStart, true);
 
             Assert.assertEquals(alignedRead.getReadName(), originalReadCopy.getReadName());

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java

@@ -363,6 +363,8 @@ public class GATKBAMIndex {
 
     private void read(final ByteBuffer buffer) {
         final int bytesRequested = buffer.limit();
+        if (bytesRequested == 0)
+            return;
 
         try {
 
@@ -379,25 +381,19 @@ public class GATKBAMIndex {
                         mFile));
             }
 
-            int totalBytesRead = 0;
+            int bytesRead = bufferedStream.read(byteArray, 0, bytesRequested);
-            // This while loop must terminate since we demand that we read at least one byte from the file at each iteration
-           while (totalBytesRead < bytesRequested) {
-                //  bufferedStream.read may return less than the requested amount of byte despite
-                // not reaching the end of the file, hence the loop.
-                int bytesRead = bufferedStream.read(byteArray, totalBytesRead, bytesRequested-totalBytesRead);
 
-                // We have a rigid expectation here to read in exactly the number of bytes we've limited
+            // We have a rigid expectation here to read in exactly the number of bytes we've limited
-                // our buffer to -- if we encounter EOF (-1), the index
+            // our buffer to -- if we encounter EOF (-1), the index
-                // must be truncated or otherwise corrupt:
+            // must be truncated or otherwise corrupt:
-                if (bytesRead <= 0) {
+            if (bytesRead <= 0) {
-                throw new UserException.MalformedFile(mFile, String.format("Premature end-of-file while reading BAM index file %s. " +
+            throw new UserException.MalformedFile(mFile, String.format("Premature end-of-file while reading BAM index file %s. " +
-                                                                           "It's likely that this file is truncated or corrupt -- " +
+                                                                       "It's likely that this file is truncated or corrupt -- " +
-                                                                           "Please try re-indexing the corresponding BAM file.",
+                                                                       "Please try re-indexing the corresponding BAM file.",
-                                                                           mFile));
+                                                                       mFile));
-                }
-                totalBytesRead += bytesRead;
             }
-            if(totalBytesRead != bytesRequested)
+
+            if(bytesRead != bytesRequested)
                 throw new RuntimeException("Read amount different from requested amount. This should not happen.");
 
             buffer.put(byteArray, 0, bytesRequested);
@@ -435,7 +431,7 @@ public class GATKBAMIndex {
             long skipped =  bufferedStream.skip(count);
 
             if( skipped != count ) { //if not managed to skip the requested amount
-		throw new ReviewedGATKException("Index: unable to reposition file channel of index file " + mFile);
+                throw new ReviewedGATKException("Index: unable to reposition file channel of index file " + mFile);
             }
         }
         catch(IOException ex) {

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java

@@ -564,7 +564,7 @@ public class SAMDataSource {
      */
     private GATKSAMIterator getIterator(SAMReaders readers, Shard shard, boolean enableVerification) {
         // Set up merging to dynamically merge together multiple BAMs.
-        Map<SAMFileReader,CloseableIterator<SAMRecord>> iteratorMap = new HashMap<SAMFileReader,CloseableIterator<SAMRecord>>();
+        Map<SamReader,CloseableIterator<SAMRecord>> iteratorMap = new HashMap<>();
 
         for(SAMReaderID id: getReaderIDs()) {
             CloseableIterator<SAMRecord> iterator = null;
@@ -1000,7 +1000,7 @@ public class SAMDataSource {
          * @param iteratorMap A map of readers to iterators.
          * @return An iterator which will merge those individual iterators.
          */
-        public MergingSamRecordIterator createMergingIterator(final Map<SAMFileReader,CloseableIterator<SAMRecord>> iteratorMap) {
+        public MergingSamRecordIterator createMergingIterator(final Map<SamReader,CloseableIterator<SAMRecord>> iteratorMap) {
             return new MergingSamRecordIterator(headerMerger,iteratorMap,true);
         }
 

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java

@@ -28,7 +28,6 @@ package org.broadinstitute.gatk.engine.datasources.reads;
 import htsjdk.samtools.seekablestream.SeekableBufferedStream;
 import htsjdk.samtools.seekablestream.SeekableFileStream;
 import org.broadinstitute.gatk.utils.BaseTest;
-import org.broadinstitute.gatk.utils.exceptions.GATKException;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -77,9 +76,13 @@ public class SeekableBufferedStreamUnitTest extends BaseTest {
     // These tests fail because SeekableBuffered stream may return _less_ than the amount you are asking for.
     // make sure that you wrap reads with while-loops.  If these test start failing (meaning that the reads work properly,
     // the layer of protection built into GATKBamIndex can be removed.
+    //
+    // pdexheimer, Jan 2015 - SeekableBufferedStream no longer returns less than the expected amount.
+    // Renaming testIndivisableSmallReadsFAIL to testIndivisableSmallReadsPASS and removing the expected exception
+    // If this bug regresses, the while loop will need to be re-introduced into GATKBamIndex.read()
 
-    @Test(dataProvider = "BasicArgumentsIndivisibleAndSmall", enabled = true, expectedExceptions = java.lang.AssertionError.class)
+    @Test(dataProvider = "BasicArgumentsIndivisibleAndSmall", enabled = true)
-    public void testIndivisableSmallReadsFAIL(Integer readLength) throws IOException {
+    public void testIndivisableSmallReadsPASS(Integer readLength) throws IOException {
         testReadsLength(readLength);
     }
 

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java

@@ -117,7 +117,7 @@ public class MalformedReadFilterUnitTest extends ReadFilterTest {
     }
 
     protected SAMRecord buildSAMRecord(final String cigarString) {
-        final Cigar nContainingCigar = TextCigarCodec.getSingleton().decode(cigarString);
+        final Cigar nContainingCigar = TextCigarCodec.decode(cigarString);
         return  this.createRead(nContainingCigar, 1, 0, 10);
     }
 

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java

@@ -40,7 +40,7 @@ public class ReadFormattingIteratorUnitTest extends BaseTest {
 
     @Test
     public void testIteratorConsolidatesCigars() {
-        final Cigar unconsolidatedCigar = TextCigarCodec.getSingleton().decode("3M0M5M0M");
+        final Cigar unconsolidatedCigar = TextCigarCodec.decode("3M0M5M0M");
         final SAMRecord unconsolidatedRead = ArtificialSAMUtils.createArtificialRead(unconsolidatedCigar);
 
         final GATKSAMIterator readIterator = GATKSAMIteratorAdapter.adapt(Arrays.asList(unconsolidatedRead).iterator());

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java

@@ -95,7 +95,7 @@ public class SAMReadCodec extends AsciiFeatureCodec<SAMReadFeature> {
         final byte[] qualities = StringUtil.stringToBytes(tokens[10]);
 
         // Infer the alignment end.
-        Cigar cigar = TextCigarCodec.getSingleton().decode(cigarString);
+        Cigar cigar = TextCigarCodec.decode(cigarString);
         int alignmentEnd = alignmentStart + cigar.getReferenceLength() - 1;
 
         // Remove printable character conversion from the qualities.

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java

@@ -28,7 +28,7 @@ package org.broadinstitute.gatk.utils.sam;
 import htsjdk.samtools.MergingSamRecordIterator;
 import htsjdk.samtools.SamFileHeaderMerger;
 import htsjdk.samtools.SAMFileHeader;
-import htsjdk.samtools.SAMFileReader;
+import htsjdk.samtools.SamReader;
 import htsjdk.samtools.SAMRecord;
 import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator;
 import org.broadinstitute.gatk.utils.iterators.GATKSAMIteratorAdapter;
@@ -69,13 +69,13 @@ public class ArtificialMultiSampleReadStream implements Iterable<SAMRecord> {
     }
 
     private void initialize() {
-        Collection<SAMFileReader> perSampleSAMReaders = new ArrayList<SAMFileReader>(perSampleArtificialReadStreams.size());
+        Collection<SamReader> perSampleSAMReaders = new ArrayList<>(perSampleArtificialReadStreams.size());
-        Collection<SAMFileHeader> headers = new ArrayList<SAMFileHeader>(perSampleArtificialReadStreams.size());
+        Collection<SAMFileHeader> headers = new ArrayList<>(perSampleArtificialReadStreams.size());
 
         for ( ArtificialSingleSampleReadStream readStream : perSampleArtificialReadStreams ) {
             Collection<SAMRecord> thisStreamReads = readStream.makeReads();
 
-            SAMFileReader reader = new ArtificialSAMFileReader(readStream.getHeader(),
+            ArtificialSAMFileReader reader = new ArtificialSAMFileReader(readStream.getHeader(),
                                                                thisStreamReads.toArray(new SAMRecord[thisStreamReads.size()]));
             perSampleSAMReaders.add(reader);
             headers.add(reader.getFileHeader());

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java

@@ -104,7 +104,7 @@ public class CigarUtils {
     }
 
     public static Cigar cigarFromString(String cigarString) {
-        return TextCigarCodec.getSingleton().decode(cigarString);
+        return TextCigarCodec.decode(cigarString);
     }
 
     /**

public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java

@@ -336,7 +336,7 @@ public class FragmentUtilsUnitTest extends BaseTest {
         final int readLen = pre + contigLen + post;
         final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, readLen);
         read.setAlignmentStart(1);
-        read.setCigar(TextCigarCodec.getSingleton().decode(pre + "S" + contigLen + "M" + post + "S"));
+        read.setCigar(TextCigarCodec.decode(pre + "S" + contigLen + "M" + post + "S"));
         read.setBaseQualities(Utils.dupBytes((byte) 30, readLen));
         read.setReadBases(Utils.dupBytes((byte)'A', readLen));
         read.setMappingQuality(60);

public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java

@@ -127,7 +127,7 @@ public class EventMapUnitTest extends BaseTest {
      */
     @Test(dataProvider = "BlockSubstitutionsData")
     public void testBlockSubstitutionsData(final String refBases, final String haplotypeBases, final String cigar, final VariantContext expectedBlock) {
-        final Haplotype hap = new Haplotype(haplotypeBases.getBytes(), false, 0, TextCigarCodec.getSingleton().decode(cigar));
+        final Haplotype hap = new Haplotype(haplotypeBases.getBytes(), false, 0, TextCigarCodec.decode(cigar));
         final GenomeLoc loc = new UnvalidatingGenomeLoc(CHR, 0, 1, refBases.length());
         final EventMap ee = new EventMap(hap, refBases.getBytes(), loc, NAME);
         ee.replaceClumpedEventsWithBlockSubstitutions();
@@ -156,7 +156,7 @@ public class EventMapUnitTest extends BaseTest {
      */
     @Test(dataProvider = "AdjacentSNPIndelTest")
     public void testAdjacentSNPIndelTest(final String refBases, final String haplotypeBases, final String cigar, final List<List<String>> expectedAlleles) {
-        final Haplotype hap = new Haplotype(haplotypeBases.getBytes(), false, 0, TextCigarCodec.getSingleton().decode(cigar));
+        final Haplotype hap = new Haplotype(haplotypeBases.getBytes(), false, 0, TextCigarCodec.decode(cigar));
         final GenomeLoc loc = new UnvalidatingGenomeLoc(CHR, 0, 1, refBases.length());
         final EventMap ee = new EventMap(hap, refBases.getBytes(), loc, NAME);
         ee.replaceClumpedEventsWithBlockSubstitutions();

public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java

@@ -167,7 +167,7 @@ public class HaplotypeUnitTest extends BaseTest {
 
     private Haplotype makeHCForCigar(final String bases, final String cigar) {
         final Haplotype h = new Haplotype(bases.getBytes());
-        h.setCigar(TextCigarCodec.getSingleton().decode(cigar));
+        h.setCigar(TextCigarCodec.decode(cigar));
         return h;
     }
 
@@ -201,10 +201,10 @@ public class HaplotypeUnitTest extends BaseTest {
 
                 final int hapStart = 10;
                 full.setAlignmentStartHapwrtRef(hapStart);
-                full.setCigar(TextCigarCodec.getSingleton().decode(full.length() + "M"));
+                full.setCigar(TextCigarCodec.decode(full.length() + "M"));
 
                 trimmed.setAlignmentStartHapwrtRef(hapStart + start);
-                trimmed.setCigar(TextCigarCodec.getSingleton().decode(trimmed.length() + "M"));
+                trimmed.setCigar(TextCigarCodec.decode(trimmed.length() + "M"));
 
                 tests.add(new Object[]{full, trimmedLoc, trimmed});
             }
@@ -212,7 +212,7 @@ public class HaplotypeUnitTest extends BaseTest {
 
         final Haplotype full = new Haplotype("ACT".getBytes(), new UnvalidatingGenomeLoc("20", 0, 10, 14));
         full.setAlignmentStartHapwrtRef(10);
-        full.setCigar(TextCigarCodec.getSingleton().decode("1M2D2M"));
+        full.setCigar(TextCigarCodec.decode("1M2D2M"));
         tests.add(new Object[]{full, new UnvalidatingGenomeLoc("20", 0, 11, 12), null});
         tests.add(new Object[]{full, new UnvalidatingGenomeLoc("20", 0, 10, 12), null});
         tests.add(new Object[]{full, new UnvalidatingGenomeLoc("20", 0, 11, 13), null});

public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java

@@ -98,7 +98,7 @@ public class LocusIteratorByStateBaseTest extends BaseTest {
         final private List<CigarElement> elements;
 
         public LIBSTest(final String cigarString) {
-            final Cigar cigar = TextCigarCodec.getSingleton().decode(cigarString);
+            final Cigar cigar = TextCigarCodec.decode(cigarString);
             this.cigarString = cigarString;
             this.elements = cigar.getCigarElements();
             this.readLength = cigar.getReadLength();

public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java

@@ -168,7 +168,7 @@ public class AlignmentUtilsUnitTest {
 
     @Test(enabled = true, dataProvider = "CalcNumDifferentBasesData")
     public void testCalcNumDifferentBases(final String cigarString, final String ref, final String read, final int expectedDifferences) {
-        final Cigar cigar = TextCigarCodec.getSingleton().decode(cigarString);
+        final Cigar cigar = TextCigarCodec.decode(cigarString);
         Assert.assertEquals(AlignmentUtils.calcNumDifferentBases(cigar, ref.getBytes(), read.getBytes()), expectedDifferences);
     }
 
@@ -299,8 +299,8 @@ public class AlignmentUtilsUnitTest {
 
     @Test(enabled = !DEBUG, dataProvider = "ConsolidateCigarData")
     public void testConsolidateCigarWithData(final String testCigarString, final String expectedCigarString) {
-        final Cigar testCigar = TextCigarCodec.getSingleton().decode(testCigarString);
+        final Cigar testCigar = TextCigarCodec.decode(testCigarString);
-        final Cigar expectedCigar = TextCigarCodec.getSingleton().decode(expectedCigarString);
+        final Cigar expectedCigar = TextCigarCodec.decode(expectedCigarString);
         final Cigar actualCigar = AlignmentUtils.consolidateCigar(testCigar);
         Assert.assertEquals(actualCigar, expectedCigar);
     }
@@ -766,8 +766,8 @@ public class AlignmentUtilsUnitTest {
 
     @Test(dataProvider = "TrimCigarData", enabled = ! DEBUG)
     public void testTrimCigar(final String cigarString, final int start, final int length, final String expectedCigarString) {
-        final Cigar cigar = TextCigarCodec.getSingleton().decode(cigarString);
+        final Cigar cigar = TextCigarCodec.decode(cigarString);
-        final Cigar expectedCigar = TextCigarCodec.getSingleton().decode(expectedCigarString);
+        final Cigar expectedCigar = TextCigarCodec.decode(expectedCigarString);
         final Cigar actualCigar = AlignmentUtils.trimCigarByReference(cigar, start, length);
         Assert.assertEquals(actualCigar, expectedCigar);
     }
@@ -801,8 +801,8 @@ public class AlignmentUtilsUnitTest {
 
     @Test(dataProvider = "TrimCigarByBasesData", enabled = !DEBUG)
     public void testTrimCigarByBase(final String cigarString, final int start, final int length, final String expectedCigarString) {
-        final Cigar cigar = TextCigarCodec.getSingleton().decode(cigarString);
+        final Cigar cigar = TextCigarCodec.decode(cigarString);
-        final Cigar expectedCigar = TextCigarCodec.getSingleton().decode(expectedCigarString);
+        final Cigar expectedCigar = TextCigarCodec.decode(expectedCigarString);
         final Cigar actualCigar = AlignmentUtils.trimCigarByBases(cigar, start, length);
         Assert.assertEquals(actualCigar, expectedCigar);
     }
@@ -853,9 +853,9 @@ public class AlignmentUtilsUnitTest {
 
     @Test(dataProvider = "ApplyCigarToCigarData", enabled = !DEBUG)
     public void testApplyCigarToCigar(final String firstToSecondString, final String secondToThirdString, final String expectedCigarString) {
-        final Cigar firstToSecond = TextCigarCodec.getSingleton().decode(firstToSecondString);
+        final Cigar firstToSecond = TextCigarCodec.decode(firstToSecondString);
-        final Cigar secondToThird = TextCigarCodec.getSingleton().decode(secondToThirdString);
+        final Cigar secondToThird = TextCigarCodec.decode(secondToThirdString);
-        final Cigar expectedCigar = TextCigarCodec.getSingleton().decode(expectedCigarString);
+        final Cigar expectedCigar = TextCigarCodec.decode(expectedCigarString);
         final Cigar actualCigar = AlignmentUtils.applyCigarToCigar(firstToSecond, secondToThird);
         Assert.assertEquals(actualCigar, expectedCigar);
     }
@@ -909,7 +909,7 @@ public class AlignmentUtilsUnitTest {
 
     @Test(dataProvider = "ReadOffsetFromCigarData", enabled = !DEBUG)
     public void testReadOffsetFromCigar(final String cigarString, final int startOnCigar, final int expectedOffset) {
-        final Cigar cigar = TextCigarCodec.getSingleton().decode(cigarString);
+        final Cigar cigar = TextCigarCodec.decode(cigarString);
         final int actualOffset = AlignmentUtils.calcFirstBaseMatchingReferenceInCigar(cigar, startOnCigar);
         Assert.assertEquals(actualOffset, expectedOffset);
     }
@@ -940,9 +940,9 @@ public class AlignmentUtilsUnitTest {
 
     @Test(dataProvider = "AddCigarElementsData", enabled = !DEBUG)
     public void testAddCigarElements(final String cigarString, final int pos, final int start, final int end, final String expectedCigarString) {
-        final Cigar cigar = TextCigarCodec.getSingleton().decode(cigarString);
+        final Cigar cigar = TextCigarCodec.decode(cigarString);
         final CigarElement elt = cigar.getCigarElement(0);
-        final Cigar expectedCigar = TextCigarCodec.getSingleton().decode(expectedCigarString);
+        final Cigar expectedCigar = TextCigarCodec.decode(expectedCigarString);
 
         final List<CigarElement> elts = new LinkedList<CigarElement>();
         final int actualEndPos = AlignmentUtils.addCigarElements(elts, pos, start, end, elt);
@@ -1000,7 +1000,7 @@ public class AlignmentUtilsUnitTest {
 
     @Test(dataProvider = "GetBasesCoveringRefIntervalData", enabled = true)
     public void testGetBasesCoveringRefInterval(final String basesString, final int refStart, final int refEnd, final String cigarString, final String expected) {
-        final byte[] actualBytes = AlignmentUtils.getBasesCoveringRefInterval(refStart, refEnd, basesString.getBytes(), 0, TextCigarCodec.getSingleton().decode(cigarString));
+        final byte[] actualBytes = AlignmentUtils.getBasesCoveringRefInterval(refStart, refEnd, basesString.getBytes(), 0, TextCigarCodec.decode(cigarString));
         if ( expected == null )
             Assert.assertNull(actualBytes);
         else
@@ -1031,13 +1031,13 @@ public class AlignmentUtilsUnitTest {
 
     @Test(dataProvider = "StartsOrEndsWithInsertionOrDeletionData", enabled = true)
     public void testStartsOrEndsWithInsertionOrDeletion(final String cigar, final boolean expected) {
-        Assert.assertEquals(AlignmentUtils.startsOrEndsWithInsertionOrDeletion(TextCigarCodec.getSingleton().decode(cigar)), expected);
+        Assert.assertEquals(AlignmentUtils.startsOrEndsWithInsertionOrDeletion(TextCigarCodec.decode(cigar)), expected);
     }
 
     @Test(dataProvider = "StartsOrEndsWithInsertionOrDeletionData", enabled = true)
     public void testRemoveTrailingDeletions(final String cigar, final boolean expected) {
 
-        final Cigar originalCigar = TextCigarCodec.getSingleton().decode(cigar);
+        final Cigar originalCigar = TextCigarCodec.decode(cigar);
         final Cigar newCigar = AlignmentUtils.removeTrailingDeletions(originalCigar);
 
         Assert.assertEquals(originalCigar.equals(newCigar), !cigar.endsWith("D"));