Examples with BeforeClass org.testng.annotations.BeforeClass used on opensource projects

Example 66 with BeforeClass

use of org.testng.annotations.BeforeClass in project gatk-protected by broadinstitute.

the class ReferenceConfidenceModelUnitTest method setUp.

@BeforeClass
public void setUp() {
    header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000);
    rg = new SAMReadGroupRecord(RGID);
    rg.setSample(sample);
    header.addReadGroup(rg);
    parser = new GenomeLocParser(header.getSequenceDictionary());
}

Example 67 with BeforeClass

use of org.testng.annotations.BeforeClass in project gatk-protected by broadinstitute.

the class ReadThreadingAssemblerUnitTest method setup.

@BeforeClass
public void setup() throws FileNotFoundException {
    seq = new CachingIndexedFastaSequenceFile(new File(hg19_chr1_1M_Reference));
    header = ArtificialReadUtils.createArtificialSamHeader(seq.getSequenceDictionary());
}

Example 68 with BeforeClass

use of org.testng.annotations.BeforeClass in project gatk by broadinstitute.

the class AnnotateTargetsIntegrationTest method createTargetFile.

@BeforeClass
public void createTargetFile() throws IOException {
    final SAMSequenceDictionary referenceDictionary = resolveReferenceDictionary();
    final List<SimpleInterval> targetIntervals = createRandomIntervals(referenceDictionary, NUMBER_OF_TARGETS, MIN_TARGET_SIZE, MAX_TARGET_SIZE, MEAN_TARGET_SIZE, TARGET_SIZE_STDEV);
    final List<Target> targets = targetIntervals.stream().map(Target::new).collect(Collectors.toList());
    TargetWriter.writeTargetsToFile(TARGET_FILE, targets);
    final Index index = IndexFactory.createIndex(TARGET_FILE, new TargetCodec(), IndexFactory.IndexType.LINEAR);
    final LittleEndianOutputStream stream = new LittleEndianOutputStream(new FileOutputStream(TARGET_FILE_IDX));
    index.write(stream);
    stream.close();
}

Example 69 with BeforeClass

use of org.testng.annotations.BeforeClass in project gatk by broadinstitute.

the class ReferenceConfidenceModelUnitTest method setUp.

@BeforeClass
public void setUp() {
    header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000);
    rg = new SAMReadGroupRecord(RGID);
    rg.setSample(sample);
    header.addReadGroup(rg);
    parser = new GenomeLocParser(header.getSequenceDictionary());
}

Example 70 with BeforeClass

use of org.testng.annotations.BeforeClass in project gatk by broadinstitute.

the class AssemblyResultSetUnitTest method init.

@BeforeClass
public void init() {
    header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000000);
    genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
}