Uses of Class
fr.ens.biologie.genomique.aozan.io.FastqSample
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Packages that use FastqSample Package Description fr.ens.biologie.genomique.aozan.collectors This package defines the collectors which collects data for a run.fr.ens.biologie.genomique.aozan.fastqscreen This package contains a module fastqscreen for the contamination detection in each sample of a run.fr.ens.biologie.genomique.aozan.io This package contains general I/O classes for Aozan. -
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Uses of FastqSample in fr.ens.biologie.genomique.aozan.collectors
Methods in fr.ens.biologie.genomique.aozan.collectors that return types with arguments of type FastqSample Modifier and Type Method Description protected Set<FastqSample>
AbstractFastqCollector. getFastqSamples()
Get the FASTQ samples.Methods in fr.ens.biologie.genomique.aozan.collectors with parameters of type FastqSample Modifier and Type Method Description protected abstract fr.ens.biologie.genomique.aozan.collectors.AbstractFastqProcessThread
AbstractFastqCollector. collectSample(RunData data, FastqSample fastqSample, File reportDir, boolean runPE)
Collect data for a fastqSample.fr.ens.biologie.genomique.aozan.collectors.AbstractFastqProcessThread
FastQCCollector. collectSample(RunData data, FastqSample fastqSample, File reportDir, boolean runPE)
fr.ens.biologie.genomique.aozan.collectors.AbstractFastqProcessThread
FastqScreenCollector. collectSample(RunData data, FastqSample fastqSample, File reportDir, boolean isRunPE)
fr.ens.biologie.genomique.aozan.collectors.AbstractFastqProcessThread
SubsetFastqCollector. collectSample(RunData data, FastqSample fastqSample, File reportDir, boolean runPE)
protected fr.ens.biologie.genomique.aozan.collectors.AbstractFastqProcessThread
UndeterminedIndexesCollector. collectSample(RunData data, FastqSample fastqSample, File reportDir, boolean runPE)
protected void
AbstractFastqCollector. saveResultPart(FastqSample fastqSample, RunData data)
Save rundata for a sample in a file in a qc report directory.protected void
SubsetFastqCollector. saveResultPart(FastqSample fastqSample, RunData data)
No data file to save in UncompressCollector.Constructors in fr.ens.biologie.genomique.aozan.collectors with parameters of type FastqSample Constructor Description SubsetFastqThread(FastqSample fastqSample, long rawClusterCount, long pfClusterCount, int numberReadsToCopy, int maxReadsToParse, int maxReadLength)
Thread constructor.UndeterminedIndexesProcessThread(RunData data, FastqSample fastqSample, File reportDir, File undeterminedIndexedXSLFile)
Constructor. -
Uses of FastqSample in fr.ens.biologie.genomique.aozan.fastqscreen
Methods in fr.ens.biologie.genomique.aozan.fastqscreen with parameters of type FastqSample Modifier and Type Method Description String
FastqScreenResult. reportToCSV(FastqSample fastqSample, String genomeSample)
Print table percent in format use by fastqscreen program with rounding value.void
FastqScreenResult. reportToHtml(FastqSample fastqSample, RunData data, String genomeSample, File reportHtml, File fastqscreenXSLFile)
Create report html file. -
Uses of FastqSample in fr.ens.biologie.genomique.aozan.io
Methods in fr.ens.biologie.genomique.aozan.io that return types with arguments of type FastqSample Modifier and Type Method Description static Set<FastqSample>
FastqSampleUtils. createListFastqSamples2(QC qc, RunData data, boolean processStandardSamples, boolean processUndeterminedSamples, boolean processOnlyFirstRead)
Create a set of FastqSample to process.
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