/**
* Prepares loggers, initiates garbage collection thread, parses arguments and initialized
* variables appropriately/
*/
private void initialize() {
fastqWriterFactory.setCreateMd5(CREATE_MD5_FILE);
switch (READ_NAME_FORMAT) {
case CASAVA_1_8:
readNameEncoder = new Casava18ReadNameEncoder(MACHINE_NAME, RUN_BARCODE, FLOWCELL_BARCODE);
break;
case ILLUMINA:
readNameEncoder = new IlluminaReadNameEncoder(RUN_BARCODE);
break;
}
final BclQualityEvaluationStrategy bclQualityEvaluationStrategy =
new BclQualityEvaluationStrategy(MINIMUM_QUALITY);
readStructure = new ReadStructure(READ_STRUCTURE);
if (MULTIPLEX_PARAMS != null) {
IOUtil.assertFileIsReadable(MULTIPLEX_PARAMS);
}
final boolean demultiplex;
if (OUTPUT_PREFIX != null) {
sampleBarcodeFastqWriterMap.put(null, buildWriter(OUTPUT_PREFIX));
demultiplex = false;
} else {
populateWritersFromMultiplexParams();
demultiplex = true;
}
final int readsPerCluster =
readStructure.templates.length() + readStructure.sampleBarcodes.length();
basecallsConverter =
new IlluminaBasecallsConverter<FastqRecordsForCluster>(
BASECALLS_DIR,
BARCODES_DIR,
LANE,
readStructure,
sampleBarcodeFastqWriterMap,
demultiplex,
MAX_READS_IN_RAM_PER_TILE / readsPerCluster,
TMP_DIR,
NUM_PROCESSORS,
FORCE_GC,
FIRST_TILE,
TILE_LIMIT,
queryNameComparator,
new FastqRecordsForClusterCodec(
readStructure.templates.length(),
readStructure.sampleBarcodes.length(),
readStructure.molecularBarcode.length()),
FastqRecordsForCluster.class,
bclQualityEvaluationStrategy,
this.APPLY_EAMSS_FILTER,
INCLUDE_NON_PF_READS,
IGNORE_UNEXPECTED_BARCODES);
log.info("READ STRUCTURE IS " + readStructure.toString());
basecallsConverter.setConverter(
new ClusterToFastqRecordsForClusterConverter(
basecallsConverter.getFactory().getOutputReadStructure()));
}
@Override
protected int doWork() {
initialize();
basecallsConverter.doTileProcessing();
return 0;
}