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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
This commit is contained in:
Phillip Dexheimer 2015-01-10 14:34:06 -05:00
parent b73e9d506a
commit 6190d660e0
16 changed files with 67 additions and 68 deletions
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16
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java
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@ -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 hap = new Haplotype(hapS.getBytes(), false, 0, TextCigarCodec.getSingleton().decode(cigar));
final Haplotype ref = new Haplotype(refS.getBytes(), true, 0, TextCigarCodec.decode(refS.length() + "M"));
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 hap1 = new Haplotype(hapS.getBytes(), false, 0, TextCigarCodec.getSingleton().decode(cigar));
final Haplotype hap2 = new Haplotype("ACGA".getBytes(), false, 0, TextCigarCodec.getSingleton().decode(cigar));
final Haplotype ref = new Haplotype(refS.getBytes(), true, 0, TextCigarCodec.decode(refS.length() + "M"));
final Haplotype hap1 = new Haplotype(hapS.getBytes(), false, 0, TextCigarCodec.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 hap1 = new Haplotype(hapS.getBytes(), false, 0, TextCigarCodec.getSingleton().decode(cigar));
final Haplotype ref = new Haplotype(refS.getBytes(), true, 0, TextCigarCodec.decode(refS.length() + "M"));
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);

4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java
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@ -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);

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java
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@ -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());

32
public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java
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@ -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;
// 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);
int bytesRead = bufferedStream.read(byteArray, 0, bytesRequested);
// 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
// must be truncated or otherwise corrupt:
if (bytesRead <= 0) {
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 -- " +
"Please try re-indexing the corresponding BAM file.",
mFile));
}
totalBytesRead += bytesRead;
// 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
// must be truncated or otherwise corrupt:
if (bytesRead <= 0) {
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 -- " +
"Please try re-indexing the corresponding BAM file.",
mFile));
}
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) {

4
public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java
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@ -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);
}

9
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java
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@ -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)
public void testIndivisableSmallReadsFAIL(Integer readLength) throws IOException {
@Test(dataProvider = "BasicArgumentsIndivisibleAndSmall", enabled = true)
public void testIndivisableSmallReadsPASS(Integer readLength) throws IOException {
testReadsLength(readLength);
}

2
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java
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@ -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);
}

2
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java
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@ -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());

2
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java
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@ -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.

8
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java
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@ -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<SAMFileHeader> headers = new ArrayList<SAMFileHeader>(perSampleArtificialReadStreams.size());
Collection<SamReader> perSampleSAMReaders = new ArrayList<>(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());

2
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java
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@ -104,7 +104,7 @@ public class CigarUtils {
}
public static Cigar cigarFromString(String cigarString) {
return TextCigarCodec.getSingleton().decode(cigarString);
return TextCigarCodec.decode(cigarString);
}
/**

2
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java
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@ -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);

4
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java
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@ -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();

8
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java
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@ -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});

2
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java
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@ -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();

32
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java
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@ -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 expectedCigar = TextCigarCodec.getSingleton().decode(expectedCigarString);
final Cigar testCigar = TextCigarCodec.decode(testCigarString);
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 expectedCigar = TextCigarCodec.getSingleton().decode(expectedCigarString);
final Cigar cigar = TextCigarCodec.decode(cigarString);
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 expectedCigar = TextCigarCodec.getSingleton().decode(expectedCigarString);
final Cigar cigar = TextCigarCodec.decode(cigarString);
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 secondToThird = TextCigarCodec.getSingleton().decode(secondToThirdString);
final Cigar expectedCigar = TextCigarCodec.getSingleton().decode(expectedCigarString);
final Cigar firstToSecond = TextCigarCodec.decode(firstToSecondString);
final Cigar secondToThird = TextCigarCodec.decode(secondToThirdString);
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"));