/** * Creates an artificial sam header with standard test parameters * * @return the sam header */ public static SAMFileHeader createArtificialSamHeader() { return createArtificialSamHeader(1, 1, 1000000); }
/** * Composes the mock up SAM file header. * * It must return an equivalent (equal) value each time it is invoked. * * @return never <code>null</code>. */ protected SAMFileHeader composeHeader() { return ArtificialSAMUtils.createArtificialSamHeader( DEFAULT_CHROMOSOME_COUNT, DEFAULT_CHROMOSOME_START_INDEX, DEFAULT_CHROMOSOME_SIZE); }
@BeforeMethod public void before() { // reset the read counter so that we are deterministic MisencodedBaseQualityReadTransformer.currentReadCounter = 0; header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000); }
@DataProvider(name = "BiasedDownsamplingTest") public Object[][] makeBiasedDownsamplingTest() { final List<Object[]> tests = new LinkedList<Object[]>(); final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000); for ( final int originalCount : Arrays.asList(1, 2, 10, 1000) ) { for ( final int toRemove : Arrays.asList(0, 1, 2, 10, 1000) ) { if ( toRemove <= originalCount ) tests.add(new Object[]{header, originalCount, toRemove}); } } return tests.toArray(new Object[][]{}); }
public Collection<SAMRecord> createReads() { Collection<SAMRecord> reads = new ArrayList<SAMRecord>(totalReads); SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000); reads.addAll(ArtificialSAMUtils.createStackOfIdenticalArtificialReads(totalReads, header, "foo", 0, 1, 100)); return reads; } }
public Collection<SAMRecord> createReads() { Collection<SAMRecord> reads = new ArrayList<SAMRecord>(totalReads); SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000); reads.addAll(ArtificialSAMUtils.createStackOfIdenticalArtificialReads(totalReads, header, "foo", 0, 1, 100)); return reads; } }
private SAMFileHeader createHeader() { SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(maxContigs, 1, (streamDensity.maxDistanceBetweenStacks + MAX_READ_LENGTH) * streamStacksPerContig.maxStacksPerContig + 100000); List<String> readGroups = new ArrayList<String>(numSamples); List<String> sampleNames = new ArrayList<String>(numSamples); for ( int i = 0; i < numSamples; i++ ) { readGroups.add("ReadGroup" + i); sampleNames.add("Sample" + i); } return ArtificialSAMUtils.createEnumeratedReadGroups(header, readGroups, sampleNames); }
@BeforeClass public void setup() throws FileNotFoundException { final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); }
@BeforeClass public void setup() throws FileNotFoundException { final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); }
@BeforeClass public void init() throws FileNotFoundException { // sequence final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 100); genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); }
@BeforeClass public void setup() throws FileNotFoundException { // sequence final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(10, 0, 10000); genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); readsDataSource = null; }
@BeforeClass public void beforeClass() { header = ArtificialSAMUtils.createArtificialSamHeader(3, 1, 10000); genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); }
public static GATKSAMRecord createArtificialRead(Cigar cigar) { int length = cigar.getReadLength(); byte [] base = {'A'}; byte [] qual = {30}; byte [] bases = Utils.arrayFromArrayWithLength(base, length); byte [] quals = Utils.arrayFromArrayWithLength(qual, length); SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(); return ArtificialSAMUtils.createArtificialRead(header, "default_read", 0, 10000, bases, quals, cigar.toString()); }
@BeforeTest public void setup() { header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000); rgForMerged = new GATKSAMReadGroupRecord("RG1"); }
@BeforeClass public void beforeClass() { header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000); genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); loc = genomeLocParser.createGenomeLoc("chr1", 1); }
@Test(dataProvider = "MergeFragmentsOffContig") public void testMergeFragmentsOffContig(final int pre1, final int post1, final int pre2, final int post2) { final int contigSize = 10; final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 0, contigSize); final GATKSAMRecord read1 = createReadOffContig(header, false, pre1, post1); final GATKSAMRecord read2 = createReadOffContig(header, true, pre2, post2); final GATKSAMRecord merged = FragmentUtils.mergeOverlappingPairedFragments(read1, read2); }
@Test (enabled = true) public void testReadWithNsRefIndexInDeletion() throws FileNotFoundException { final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); final int readLength = 76; final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 8975, readLength); read.setReadBases(Utils.dupBytes((byte) 'A', readLength)); read.setBaseQualities(Utils.dupBytes((byte)30, readLength)); read.setCigarString("3M414N1D73M"); final int result = ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, 9392, ReadUtils.ClippingTail.LEFT_TAIL); Assert.assertEquals(result, 2); }
@BeforeClass public void beforeClass() { header = ArtificialSAMUtils.createArtificialSamHeader((endingChr - startingChr) + 1, startingChr, readCount + DEFAULT_READ_LENGTH); contig = header.getSequence(0).getSequenceName(); genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); initializeTests(); }
@BeforeMethod public void doBefore() { header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000); genomeLocParser =new GenomeLocParser(header.getSequenceDictionary()); engine = new GenomeAnalysisEngine(); engine.setReferenceDataSource(refFile); engine.setGenomeLocParser(genomeLocParser); obj.initialize(engine, null); }
@Test public void testEmptyIntervalSetHandling() throws Exception { GenomeLocParser genomeLocParser = new GenomeLocParser(ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000).getSequenceDictionary()); GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine(); testEngine.setWalker(new TestCountReadsWalker()); testEngine.setIntervals(new GenomeLocSortedSet(genomeLocParser)); testEngine.validateSuppliedIntervals(); }