Package fr.ens.biologie.genomique.aozan.fastqc

Class RuntimePatchFastQC

java.lang.Object

fr.ens.biologie.genomique.aozan.fastqc.RuntimePatchFastQC

public class RuntimePatchFastQC
extends Object

This class redefine methods or constructors from FastQC to provide access to files in fastqc jar. Fix bug with FastQC version 0.10.1

Since:

1.1

Author:

Laurent Jourdren, Sandrine Perrin

Constructor Summary

Constructors

Constructor	Description
RuntimePatchFastQC()

Method Summary

Modifier and Type	Method	Description
static void	changeSuperClassOverrepresentedModule(boolean useBlast)	Change superclass of Overrepresented Module from FastQC v0.11.2 to replace a new class, it add a link html to ncbi website in result table.
static void	rewriteContaminantFinderMethod(boolean useBlast)	Add code at the beginning on the method.
static void	runPatchFastQC()	Execute method who patch code from FastQC before call in Aozan.
static void	runPatchFastQC(boolean useBlast)	Execute method who patch code from FastQC before call in Aozan.

Methods inherited from class java.lang.Object

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

Constructor Detail

RuntimePatchFastQC

public RuntimePatchFastQC()

Method Detail

rewriteContaminantFinderMethod

public static void rewriteContaminantFinderMethod(boolean useBlast)
                                           throws javassist.CannotCompileException

Add code at the beginning on the method. ContaminentFinder.findContaminantHit to call the version Aozan of this method which had access to the contaminant list in fastqc jar.

Parameters:

useBlast - the as blast to use

Throws:

javassist.CannotCompileException - thrown when bytecode transformation has failed.

changeSuperClassOverrepresentedModule

public static void changeSuperClassOverrepresentedModule(boolean useBlast)
                                                  throws javassist.CannotCompileException

Change superclass of Overrepresented Module from FastQC v0.11.2 to replace a new class, it add a link html to ncbi website in result table.

Parameters:

useBlast - true if use blast to search source on overepresented sequences

Throws:

javassist.CannotCompileException - thrown when bytecode transformation has failed.

runPatchFastQC

public static void runPatchFastQC()
                           throws AozanException

Execute method who patch code from FastQC before call in Aozan.

Throws:

AozanException - throw an error occurs during modification bytecode fastqc

runPatchFastQC

public static void runPatchFastQC(boolean useBlast)
                           throws AozanException

Execute method who patch code from FastQC before call in Aozan.

Parameters:

useBlast - if blast will be used else false

Throws:

AozanException - throw an error occurs during modification bytecode fastqc