/**
* There are multiple parsers for the same IlluminaDataType (e.g. BCLParser and QSeqParser).
* Instantiate an instance of the preferred parser for the given data type with the information
* available and return it.
*
* @param format The type of data we want to parse
* @param requestedTiles The requestedTiles over which we will be parsing data
* @return A parser that will parse dataType data over the given requestedTiles and cycles and
* output it in groupings of the sizes specified in outputLengths
*/
private IlluminaParser makeParser(
final SupportedIlluminaFormat format, final List<Integer> requestedTiles) {
final IlluminaParser parser;
switch (format) {
case Barcode:
parser =
new BarcodeParser(
((PerTileFileUtil) fileUtil.getUtil(SupportedIlluminaFormat.Barcode))
.getFiles(requestedTiles));
break;
case Bcl:
{
final CycleIlluminaFileMap bclFileMap =
((PerTilePerCycleFileUtil) fileUtil.getUtil(SupportedIlluminaFormat.Bcl))
.getFiles(requestedTiles, outputMapping.getOutputCycles());
bclFileMap.assertValid(requestedTiles, outputMapping.getOutputCycles());
parser =
new BclParser(
basecallDirectory,
lane,
bclFileMap,
outputMapping,
this.applyEamssFiltering,
bclQualityEvaluationStrategy);
break;
}
case Filter:
final IlluminaFileMap filterFileMap =
((PerTileFileUtil) fileUtil.getUtil(SupportedIlluminaFormat.Filter))
.getFiles(requestedTiles);
parser = new FilterParser(filterFileMap);
break;
case Locs:
case Clocs:
case Pos:
final PerTileFileUtil fu = (PerTileFileUtil) fileUtil.getUtil(format);
parser = new PosParser(fu.getFiles(requestedTiles), format);
break;
case MultiTileFilter:
parser =
((MultiTileFilterFileUtil) fileUtil.getUtil(SupportedIlluminaFormat.MultiTileFilter))
.makeParser(requestedTiles);
break;
case MultiTileLocs:
parser =
((MultiTileLocsFileUtil) fileUtil.getUtil(SupportedIlluminaFormat.MultiTileLocs))
.makeParser(requestedTiles);
break;
case MultiTileBcl:
{
final MultiTileBclFileUtil util =
(MultiTileBclFileUtil) fileUtil.getUtil(SupportedIlluminaFormat.MultiTileBcl);
final CycleIlluminaFileMap bclFileMap =
util.getFiles(requestedTiles, outputMapping.getOutputCycles());
bclFileMap.assertValid(requestedTiles, outputMapping.getOutputCycles());
parser =
new MultiTileBclParser(
basecallDirectory,
lane,
bclFileMap,
outputMapping,
this.applyEamssFiltering,
bclQualityEvaluationStrategy,
util.tileIndex);
break;
}
default:
throw new PicardException(
"Unrecognized data type(" + format + ") found by IlluminaDataProviderFactory!");
}
return parser;
}
/**
* Sometimes (in the case of skipped reads) the logical read structure of the output cluster data
* is different from the input readStructure
*
* @return The ReadStructure describing the output cluster data
*/
public ReadStructure getOutputReadStructure() {
return outputMapping.getOutputReadStructure();
}
