Package fr.ens.biologie.genomique.aozan.aozan3.dataprocessor

Class DoradoONTBasecallingDataProcessor

java.lang.Object

fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DoradoONTBasecallingDataProcessor

All Implemented Interfaces:

DataProcessor

public class DoradoONTBasecallingDataProcessor
extends Object
implements DataProcessor

This class implements a Dorado data processor.

Since:

3.1

Author:

Laurent Jourdren

Nested Class Summary

Nested classes/interfaces inherited from interface fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessor

DataProcessor.ProcessResult

Field Summary

Fields

Modifier and Type	Field	Description
static String	PROCESSOR_NAME

Constructor Summary

Constructors

Constructor	Description
DoradoONTBasecallingDataProcessor()

Method Summary

Modifier and Type	Method	Description
Set<DataTypeFilter>	getInputRequirements()	Get the input requirements of the processor.
String	getName()	Get the name of the processor.
void	init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)	Initialize the processor.
DataProcessor.ProcessResult	process(InputData inputData, RunConfiguration runConf)	Process data.
static void	run(Path inputTar, Path outputPath, Path modelsPath, String runId, String doradoVersion, Path tmpPath, String flowcellType, String kit, String barcodeKits, boolean trimBarcodes, String minQscore, String model, String cudaDevice, int batchSize, int chunkSize, boolean keepTemporaryFiles, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

PROCESSOR_NAME

public static final String PROCESSOR_NAME

See Also:

Constant Field Values

Constructor Detail

DoradoONTBasecallingDataProcessor

public DoradoONTBasecallingDataProcessor()

Method Detail

getName

public String getName()

Description copied from interface: DataProcessor

Get the name of the processor.

Specified by:

getName in interface DataProcessor

Returns:

the name of the processor

init

public void init(Configuration conf,
                 fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
          throws Aozan3Exception

Description copied from interface: DataProcessor

Initialize the processor.

Specified by:

init in interface DataProcessor

Parameters:

conf - the configuration of the processor

logger - the logger to use

Throws:

Aozan3Exception - if an error occurs while initialize the processor

getInputRequirements

public Set<DataTypeFilter> getInputRequirements()

Description copied from interface: DataProcessor

Get the input requirements of the processor.

Specified by:

getInputRequirements in interface DataProcessor

Returns:

a set with input requirements

process

public DataProcessor.ProcessResult process(InputData inputData,
                                           RunConfiguration runConf)
                                    throws Aozan3Exception

Description copied from interface: DataProcessor

Process data.

Specified by:

process in interface DataProcessor

Parameters:

inputData - input run data

runConf - run configuration

Returns:

a ProcessResult object

Throws:

Aozan3Exception - if an error occurs while processing the data

run

public static void run(Path inputTar,
                       Path outputPath,
                       Path modelsPath,
                       String runId,
                       String doradoVersion,
                       Path tmpPath,
                       String flowcellType,
                       String kit,
                       String barcodeKits,
                       boolean trimBarcodes,
                       String minQscore,
                       String model,
                       String cudaDevice,
                       int batchSize,
                       int chunkSize,
                       boolean keepTemporaryFiles,
                       fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
                throws Aozan3Exception

Parameters:

inputTar - input tar file

outputPath - output directory

modelsPath - directory with models for Dorado

runId - run Id

doradoVersion - dorado version

tmpPath - tempoary directory

flowcellType - flowcell type

kit - kit type

barcodeKits - barcode kit used

trimBarcodes - true if barcode must be trimmed

minQscore - minimal Q score

model - model to use

cudaDevice - CUDA device

batchSize - batch size

chunkSize - chunk size

keepTemporaryFiles - true to keep temporary files

logger - logger to use

Throws:

Aozan3Exception - if an error occurs while executing the basecalling