Package fr.ens.biologie.genomique.aozan.fastqscreen

Class FastqScreenResult

java.lang.Object

fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenResult

public class FastqScreenResult
extends Object

This class manages results from fastqscreen.

Since:

1.0

Author:

Sandrine Perrin

Method Summary

Modifier and Type	Method	Description
void	addGenome(String genome, String genomeSample)	Update the list of reference genome used by fastqscreen.
void	countHitPerGenome(String genome, boolean oneHit, boolean oneGenome)	Count for each read number of hit per reference genome.
void	countPercentValue(int readsMapped, int readsprocessed)	Convert values from fastqscreen in percentage.
RunData	createRundata(String prefix)	Update rundata with results from fastqscreen.
int	getCountReadsMapped()
int	getCountReadsProcessed()
String	reportToCSV(FastqSample fastqSample, String genomeSample)	Print table percent in format use by fastqscreen program with rounding value.
void	reportToHtml(FastqSample fastqSample, RunData data, String genomeSample, File reportHtml, File fastqscreenXSLFile)	Create report html file.

Methods inherited from class java.lang.Object

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

Method Detail

reportToCSV

public String reportToCSV(FastqSample fastqSample,
                          String genomeSample)
                   throws AozanException

Print table percent in format use by fastqscreen program with rounding value.

Returns:

string with results from fastqscreen

Throws:

AozanException

reportToHtml

public void reportToHtml(FastqSample fastqSample,
                         RunData data,
                         String genomeSample,
                         File reportHtml,
                         File fastqscreenXSLFile)
                  throws AozanException,
                         IOException

Create report html file.

Parameters:

fastqSample - fastqSample instance

data - object rundata on the run

genomeSample - genome reference corresponding to sample

fastqscreenXSLFile - xsl file, can be null to use default file

Throws:

AozanException - if an error occurs during creation document xml or transforming document xml in html file

IOException - if an error occurs during paring the xsl file

addGenome

public void addGenome(String genome,
                      String genomeSample)

Update the list of reference genome used by fastqscreen.

Parameters:

genome - name of new reference genome

genomeSample - genome reference corresponding to sample

countHitPerGenome

public void countHitPerGenome(String genome,
                              boolean oneHit,
                              boolean oneGenome)

Count for each read number of hit per reference genome.

Parameters:

genome - genome name

oneHit - true if read mapped one time on genome else false

oneGenome - true if read mapped on several genome else false

countPercentValue

public void countPercentValue(int readsMapped,
                              int readsprocessed)
                       throws AozanException

Convert values from fastqscreen in percentage.

Parameters:

readsMapped - number reads mapped

readsprocessed - number reads total

Throws:

AozanException - if no value

createRundata

public RunData createRundata(String prefix)
                      throws AozanException

Update rundata with results from fastqscreen.

Parameters:

prefix - name of sample

Throws:

AozanException - if no value.

getCountReadsMapped

public int getCountReadsMapped()

getCountReadsProcessed

public int getCountReadsProcessed()