Examples with AlignmentOutput com.hartwig.pipeline.alignment.AlignmentOutput used on opensource projects

Example 6 with AlignmentOutput

use of com.hartwig.pipeline.alignment.AlignmentOutput in project pipeline5 by hartwigmedical.

the class SingleSamplePipeline method convertCramsIfNecessary.

private AlignmentOutput convertCramsIfNecessary(final Arguments arguments, final SingleSampleRunMetadata metadata, final PipelineState state) throws Exception {
    AlignmentOutput alignmentOutput = report.add(state.add(aligner.run(metadata)));
    alignmentOutput = state.shouldProceed() && !arguments.useCrams() && alignmentOutput.alignments().path().endsWith(FileTypes.CRAM) ? state.add(stageRunner.run(metadata, new Cram2Bam(alignmentOutput.alignments(), metadata.type()))) : alignmentOutput;
    return alignmentOutput;
}

Example 7 with AlignmentOutput

use of com.hartwig.pipeline.alignment.AlignmentOutput in project pipeline5 by hartwigmedical.

the class PersistedAlignmentTest method returnsBamsInConventionalLocationIfNoPersisted.

@Test
public void returnsBamsInConventionalLocationIfNoPersisted() {
    PersistedAlignment victim = new PersistedAlignment(new NoopPersistedDataset(), Arguments.testDefaults());
    AlignmentOutput output = victim.run(TestInputs.referenceRunMetadata());
    assertThat(output.sample()).isEqualTo("reference");
    assertThat(output.status()).isEqualTo(PipelineStatus.PERSISTED);
    assertThat(output.alignments()).isEqualTo(GoogleStorageLocation.of("bucket", "set/reference/aligner/reference.bam"));
}