Examples with TargetCodec org.broadinstitute.hellbender.utils.codecs.TargetCodec used on opensource projects

Example 1 with TargetCodec

use of org.broadinstitute.hellbender.utils.codecs.TargetCodec 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 2 with TargetCodec

use of org.broadinstitute.hellbender.utils.codecs.TargetCodec in project gatk-protected 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();
}