Class FastqScreenResult
- java.lang.Object
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- fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenResult
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public class FastqScreenResult extends Object
This class manages results from fastqscreen.- Since:
- 1.0
- Author:
- Sandrine Perrin
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Method Summary
All Methods Instance Methods Concrete Methods 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.
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Method Detail
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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
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reportToHtml
public void reportToHtml(FastqSample fastqSample, RunData data, String genomeSample, File reportHtml, File fastqscreenXSLFile) throws AozanException, IOException
Create report html file.- Parameters:
fastqSample
- fastqSample instancedata
- object rundata on the rungenomeSample
- genome reference corresponding to samplefastqscreenXSLFile
- 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 fileIOException
- if an error occurs during paring the xsl file
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addGenome
public void addGenome(String genome, String genomeSample)
Update the list of reference genome used by fastqscreen.- Parameters:
genome
- name of new reference genomegenomeSample
- genome reference corresponding to sample
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countHitPerGenome
public void countHitPerGenome(String genome, boolean oneHit, boolean oneGenome)
Count for each read number of hit per reference genome.- Parameters:
genome
- genome nameoneHit
- true if read mapped one time on genome else falseoneGenome
- true if read mapped on several genome else false
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countPercentValue
public void countPercentValue(int readsMapped, int readsprocessed) throws AozanException
Convert values from fastqscreen in percentage.- Parameters:
readsMapped
- number reads mappedreadsprocessed
- number reads total- Throws:
AozanException
- if no value
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createRundata
public RunData createRundata(String prefix) throws AozanException
Update rundata with results from fastqscreen.- Parameters:
prefix
- name of sample- Throws:
AozanException
- if no value.
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getCountReadsMapped
public int getCountReadsMapped()
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getCountReadsProcessed
public int getCountReadsProcessed()
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