/** * Index the given input files. By default, executes the steps in {@link VariantStoragePipeline}. * * Will create a {@link #newStoragePipeline} for each input file. * * @param inputFiles Input files to index * @param outdirUri Output directory for possible intermediate files * @param doExtract Execute extract step {@link VariantStoragePipeline#extract} * @param doTransform Execute transform step {@link VariantStoragePipeline#transform} * @param doLoad Execute load step {@link VariantStoragePipeline#load} * @return List of {@link StoragePipelineResult}, one for each input file. * @throws StorageEngineException If there is any problem related with the StorageEngine */ @Override public List<StoragePipelineResult> index(List<URI> inputFiles, URI outdirUri, boolean doExtract, boolean doTransform, boolean doLoad) throws StorageEngineException { List<StoragePipelineResult> results = super.index(inputFiles, outdirUri, doExtract, doTransform, doLoad); if (doLoad) { annotateLoadedFiles(outdirUri, inputFiles, results, getOptions()); calculateStatsForLoadedFiles(outdirUri, inputFiles, results, getOptions()); searchIndexLoadedFiles(inputFiles, getOptions()); } return results; }