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

Class CopyAndMergeGuppyOutput

java.lang.Object

fr.ens.biologie.genomique.aozan.aozan3.util.CopyAndMergeGuppyOutput

public class CopyAndMergeGuppyOutput
extends Object

Merge FASTQ files from a directory in another directory.

Since:

3.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
CopyAndMergeGuppyOutput(Path inputPath, Path outputPath)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	execute()	Execute the copy and merge FASTQ files.
boolean	isCompressLogs()	Test if log compression is enabled.
boolean	isCompressSequencingSummary()	Test if log sequencing summary file compression is enabled.
boolean	isCompressSequencingTelemetry()	Test if log telemetry file compression is enabled.
boolean	isFastqMergin()	Test if FASTQ merging is enabled.
boolean	isLogMerging()	Test if logs merging is enabled.
void	setCompressLogs(boolean compressLogs)	Enable log files compression.
void	setCompressSequencingSummary(boolean compressSequencingSummary)	Enable sequencing summary file compression.
void	setCompressTelemetry(boolean compressTelemetry)	Enable telemetry file compression.
void	setFastqMerging(boolean mergeFastq)	Enable the FASTQ files merging.
void	setLogMerging(boolean mergeLog)	Enable the log files merging.

Methods inherited from class java.lang.Object

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

Constructor Detail

CopyAndMergeGuppyOutput

public CopyAndMergeGuppyOutput(Path inputPath,
                               Path outputPath)
                        throws IOException

Constructor.

Parameters:

inputPath - input path to copy

outputPath - output path to copy

Throws:

IOException - if path are not valid

Method Detail

isFastqMergin

public boolean isFastqMergin()

Test if FASTQ merging is enabled.

Returns:

true if FASTQ merging is enabled

isLogMerging

public boolean isLogMerging()

Test if logs merging is enabled.

Returns:

true if logs merging is enabled

isCompressLogs

public boolean isCompressLogs()

Test if log compression is enabled.

Returns:

true if log compression is enabled

isCompressSequencingTelemetry

public boolean isCompressSequencingTelemetry()

Test if log telemetry file compression is enabled.

Returns:

true if telemetry file compression is enabled

isCompressSequencingSummary

public boolean isCompressSequencingSummary()

Test if log sequencing summary file compression is enabled.

Returns:

true if sequencing summary file compression is enabled

setFastqMerging

public void setFastqMerging(boolean mergeFastq)

Enable the FASTQ files merging.

Parameters:

mergeFastq - true to merge FASTQ file

setLogMerging

public void setLogMerging(boolean mergeLog)

Enable the log files merging.

Parameters:

mergeLog - true to merge log files

setCompressLogs

public void setCompressLogs(boolean compressLogs)

Enable log files compression.

Parameters:

compressLogs - true to compress log files

setCompressTelemetry

public void setCompressTelemetry(boolean compressTelemetry)

Enable telemetry file compression.

Parameters:

compressTelemetry - true to compress telemetry file

setCompressSequencingSummary

public void setCompressSequencingSummary(boolean compressSequencingSummary)

Enable sequencing summary file compression.

Parameters:

compressSequencingSummary - true to compress sequencing summary file

execute

public void execute()
             throws IOException

Execute the copy and merge FASTQ files.

Throws:

IOException - if an error occurs while copying and merging files