@Override
protected void setupPipeline(Pipeline pipeline) {
// Load the reads.
final ReadsDataflowSource readsDataflowSource = new ReadsDataflowSource(bam, pipeline);
final SAMFileHeader readsHeader = readsDataflowSource.getHeader();
final List<SimpleInterval> intervals =
intervalArgumentCollection.intervalsSpecified()
? intervalArgumentCollection.getIntervals(readsHeader.getSequenceDictionary())
: IntervalUtils.getAllIntervalsForReference(readsHeader.getSequenceDictionary());
final PCollectionView<SAMFileHeader> headerSingleton =
ReadsDataflowSource.getHeaderView(pipeline, readsHeader);
final PCollection<GATKRead> initialReads = readsDataflowSource.getReadPCollection(intervals);
// Apply MarkDuplicates to produce updated GATKReads.
final PCollection<GATKRead> markedReads =
initialReads.apply(new MarkDuplicates(headerSingleton));
// Load the Variants and the Reference and join them to reads.
final VariantsDataflowSource variantsDataflowSource =
new VariantsDataflowSource(baseRecalibrationKnownVariants, pipeline);
Map<String, String> referenceNameToIdTable =
RefAPISource.buildReferenceNameToIdTable(pipeline.getOptions(), referenceName);
RefAPIMetadata refAPIMetadata = new RefAPIMetadata(referenceName, referenceNameToIdTable);
final PCollection<KV<GATKRead, ReadContextData>> readsWithContext =
AddContextDataToRead.add(markedReads, refAPIMetadata, variantsDataflowSource);
// Apply BQSR.
final PCollection<RecalibrationTables> recalibrationReports =
readsWithContext.apply(new BaseRecalibratorStub(headerSingleton));
final PCollectionView<RecalibrationTables> mergedRecalibrationReport =
recalibrationReports.apply(View.<RecalibrationTables>asSingleton());
final PCollection<GATKRead> finalReads =
markedReads.apply(new ApplyBQSRStub(headerSingleton, mergedRecalibrationReport));
SmallBamWriter.writeToFile(pipeline, finalReads, readsHeader, output);
}