Uses of Class
fr.ens.biologie.genomique.aozan.RunData
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Packages that use RunData Package Description fr.ens.biologie.genomique.aozan Root package of Aozan.fr.ens.biologie.genomique.aozan.collectors This package defines the collectors which collects data for a run.fr.ens.biologie.genomique.aozan.collectors.interop This package defines the collectors which collects data from InterOp binary files for a run.fr.ens.biologie.genomique.aozan.collectors.stats This package defines the statistics 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.fr.ens.biologie.genomique.aozan.tests.global This package contains class of global tests which defines the collector to launch and creates a report of a quality control.fr.ens.biologie.genomique.aozan.tests.lane This package contains class of lane tests which defines the collector to launch and creates a report of a quality control.fr.ens.biologie.genomique.aozan.tests.pooledsample This package contains class of project tests which defines the collector to launch and creates a report of a quality control.fr.ens.biologie.genomique.aozan.tests.project This package contains class of project tests which defines the collector to launch and creates a report of a quality control.fr.ens.biologie.genomique.aozan.tests.sample This package contains class of sample tests which defines the collector to launch and creates a report of a quality control.fr.ens.biologie.genomique.aozan.util This package utility classes. -
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Uses of RunData in fr.ens.biologie.genomique.aozan
Methods in fr.ens.biologie.genomique.aozan that return RunData Modifier and Type Method Description RunData
RunDataGenerator. collect(QC qc)
Collect data and return a RunData object.RunData
QCReport. getData()
Get the data.Methods in fr.ens.biologie.genomique.aozan with parameters of type RunData Modifier and Type Method Description void
RunData. put(RunData data)
Set the key and values of a RunData object in the current RunData.Constructors in fr.ens.biologie.genomique.aozan with parameters of type RunData Constructor Description PooledSampleComparator(RunData data)
Constructor.ProjectComparator(RunData data)
Constructor.QCReport(RunData data, List<GlobalTest> globalTests, List<LaneTest> laneTests, List<ProjectTest> projectStatsTests, List<PooledSampleTest> samplesStatsTests, List<SampleTest> sampleTests)
Public constructor.RunData(RunData data)
Public constructor. -
Uses of RunData in fr.ens.biologie.genomique.aozan.collectors
Methods in fr.ens.biologie.genomique.aozan.collectors with parameters of type RunData Modifier and Type Method Description void
AbstractFastqCollector. collect(RunData data)
Collect data : browse data for call concrete collector.void
AozanCollector. collect(RunData data)
void
Collector. collect(RunData data)
Collect data.void
DemultiplexingCollector. collect(RunData data)
void
DemultiplexStatsCollector. collect(RunData data)
void
GlobalStatsCollector. collect(RunData data)
void
MultiQCCollector. collect(RunData data)
void
PrimaryAnalysisMetricsCollector. collect(RunData data)
void
ReadCollector. collect(RunData data)
void
RunInfoCollector. collect(RunData data)
void
SamplesheetCollector. collect(RunData data)
void
StatisticsCollector. collect(RunData data)
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)
abstract Map<Integer,EntityStat>
StatisticsCollector. extractEntityStats(RunData data)
Extract entity stats.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 RunData Constructor Description UndeterminedIndexesProcessThread(RunData data, FastqSample fastqSample, File reportDir, File undeterminedIndexedXSLFile)
Constructor. -
Uses of RunData in fr.ens.biologie.genomique.aozan.collectors.interop
Methods in fr.ens.biologie.genomique.aozan.collectors.interop with parameters of type RunData Modifier and Type Method Description void
ErrorMetricsCollector. collect(RunData data)
Collect data.void
ExtractionMetricsCollector. collect(RunData data)
Collect data from TileMetric interOpFile.void
QualityMetricsCollector. collect(RunData data)
Collect data from QualityMetric interOpFile.void
TileMetricsCollector. collect(RunData data)
Collect data from TileMetric interOpFile. -
Uses of RunData in fr.ens.biologie.genomique.aozan.collectors.stats
Methods in fr.ens.biologie.genomique.aozan.collectors.stats with parameters of type RunData Modifier and Type Method Description Map<Integer,EntityStat>
ProjectStatisticsCollector. extractEntityStats(RunData data)
Map<Integer,EntityStat>
SampleStatisticsCollector. extractEntityStats(RunData data)
Constructors in fr.ens.biologie.genomique.aozan.collectors.stats with parameters of type RunData Constructor Description EntityStat(RunData runData, int projectId, int sampleId, StatisticsCollector statCollector)
Instantiates a new entity stat.EntityStat(RunData runData, int projectId, StatisticsCollector statCollector)
Instantiates a new project stat. -
Uses of RunData in fr.ens.biologie.genomique.aozan.fastqscreen
Methods in fr.ens.biologie.genomique.aozan.fastqscreen that return RunData Modifier and Type Method Description RunData
FastqScreenResult. createRundata(String prefix)
Update rundata with results from fastqscreen.Methods in fr.ens.biologie.genomique.aozan.fastqscreen with parameters of type RunData Modifier and Type Method Description void
FastqScreenResult. reportToHtml(FastqSample fastqSample, RunData data, String genomeSample, File reportHtml, File fastqscreenXSLFile)
Create report html file. -
Uses of RunData in fr.ens.biologie.genomique.aozan.io
Methods in fr.ens.biologie.genomique.aozan.io with parameters of type RunData 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. -
Uses of RunData in fr.ens.biologie.genomique.aozan.tests.global
Methods in fr.ens.biologie.genomique.aozan.tests.global with parameters of type RunData Modifier and Type Method Description TestResult
AbstractSimpleGlobalTest. test(RunData data)
TestResult
ClusterDensityGlobalTest. test(RunData data)
TestResult
ClusterDensityPFGlobalTest. test(RunData data)
TestResult
ErrorRateGlobalTest. test(RunData data)
TestResult
GlobalTest. test(RunData data)
Do a test.TestResult
OccupancyPercentGlobalTest. test(RunData data)
TestResult
ProjectCountGlobalTest. test(RunData data)
TestResult
Q30PercentGlobalTest. test(RunData data)
TestResult
SampleCountGlobalTest. test(RunData data)
TestResult
UndeterminedClusterPercentGlobalTest. test(RunData data)
protected Number
AbstractSimpleGlobalTest. transformValue(Number value, RunData data)
Transform the value.protected Number
BaseCountGlobalTest. transformValue(Number value, RunData data)
protected Number
CycleCountGlobalTest. transformValue(Number value, RunData data)
protected Number
LaneCountGlobalTest. transformValue(Number value, RunData data)
protected Number
LoadingConcentrationPercentGlobalTest. transformValue(Number value, RunData data)
protected Number
MeanPFClusterCountGlobalTest. transformValue(Number value, RunData data)
protected Number
MeanPhiXRawClusterCountGlobalTest. transformValue(Number value, RunData data)
protected Number
MeanRawClusterCountGlobalTest. transformValue(Number value, RunData data)
protected Number
MedianPFClusterCountGlobalTest. transformValue(Number value, RunData data)
protected Number
MedianPhiXRawClusterCountGlobalTest. transformValue(Number value, RunData data)
protected Number
MedianRawClusterCountGlobalTest. transformValue(Number value, RunData data)
protected Number
NonIndexedBaseCountGlobalTest. transformValue(Number value, RunData data)
protected Number
PFClusterCountGlobalTest. transformValue(Number value, RunData data)
protected Number
PFClusterPercentGlobalTest. transformValue(Number value, RunData data)
protected Number
PFClusterSDGlobalTest. transformValue(Number value, RunData data)
protected Number
PhiXAlignPercentGlobalTest. transformValue(Number value, RunData data)
protected Number
PhiXRawClusterCountGlobalTest. transformValue(Number value, RunData data)
protected Number
PhiXRawClusterSDGlobalTest. transformValue(Number value, RunData data)
protected Number
RawClusterCountGlobalTest. transformValue(Number value, RunData data)
protected Number
RawClusterSDGlobalTest. transformValue(Number value, RunData data)
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Uses of RunData in fr.ens.biologie.genomique.aozan.tests.lane
Methods in fr.ens.biologie.genomique.aozan.tests.lane with parameters of type RunData Modifier and Type Method Description TestResult
AbstractSimpleLaneTest. test(RunData data, int read, boolean indexedRead, int lane)
TestResult
LaneTest. test(RunData data, int read, boolean indexedRead, int lane)
Do a test.TestResult
PFClusterPercentLaneTest. test(RunData data, int read, boolean indexedRead, int lane)
TestResult
PhasingPrephasingPercentLaneTest. test(RunData data, int read, boolean indexedRead, int lane)
TestResult
PhiXAlignPercentLaneTest. test(RunData data, int read, boolean indexedRead, int lane)
TestResult
PhiXRawClusterCountLaneTest. test(RunData data, int read, boolean indexedRead, int lane)
TestResult
Q30PercentLaneTest. test(RunData data, int read, boolean indexedRead, int lane)
protected Number
AbstractSimpleLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
Transform the value.protected Number
ClusterDensityLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
protected Number
ClusterDensityPFLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
protected Number
Cycle100ErrorRateLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
protected Number
Cycle20IntensityPercentLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
protected Number
Cycle35ErrorRateLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
protected Number
Cycle75ErrorRateLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
protected Number
DensityLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
protected Number
ErrorRateLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
protected Number
OccupancyPercentLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
protected Number
PFClusterCountLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
protected Number
RawClusterCountLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
protected Number
YieldLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
protected Number
YieldPFLaneTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
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Uses of RunData in fr.ens.biologie.genomique.aozan.tests.pooledsample
Methods in fr.ens.biologie.genomique.aozan.tests.pooledsample with parameters of type RunData Modifier and Type Method Description TestResult
AbstractSimpleSampleTest. test(RunData data, int pooledSampleId)
TestResult
FastQScreenMappedExceptRefPercentPooledSampleTest. test(RunData data, int pooledSampleId)
TestResult
FastQScreenMappedPercentPooledSampleTest. test(RunData data, int pooledSampleId)
TestResult
FastQScreenReportPooledSampleTest. test(RunData data, int pooledSampleId)
TestResult
FastQScreenSampleOvercontaminationCountPooledSampleTest. test(RunData data, int pooledSampleId)
TestResult
InProjectPercentPooledSampleTest. test(RunData data, int pooledSampleId)
TestResult
InRunPercentPooledSampleTest. test(RunData data, int pooledSampleId)
TestResult
PFBaseMeanQualityScorePooledSampleTest. test(RunData data, int pooledSampleId)
TestResult
PFPercentPooledSampleTest. test(RunData data, int pooledSampleId)
TestResult
PooledSampleTest. test(RunData data, int pooledSampleId)
Do a test.TestResult
Q30PercentPooledSampleTest. test(RunData data, int pooledSampleId)
TestResult
RecoverablePFClusterPercentPooledSampleTest. test(RunData data, int pooledSampleId)
TestResult
RecoverableRawClusterPercentPooledSampleTest. test(RunData data, int pooledSampleId)
TestResult
SampleInPoolCountPooledSampleTest. test(RunData data, int pooledSampleId)
protected Number
AbstractSimpleSampleTest. transformValue(Number value, RunData data)
Transform the value. -
Uses of RunData in fr.ens.biologie.genomique.aozan.tests.project
Methods in fr.ens.biologie.genomique.aozan.tests.project with parameters of type RunData Modifier and Type Method Description TestResult
AbstractSimpleProjectTest. test(RunData data, int projectId)
TestResult
FastQScreenReportProjectTest. test(RunData data, int projectId)
TestResult
MultiQCReportProjectTest. test(RunData data, int projectId)
TestResult
ProjectTest. test(RunData data, int projectId)
Do a test.TestResult
RecoverablePFClusterPercentProjectTest. test(RunData data, int projectId)
TestResult
RecoverableRawClusterPercentProjectTest. test(RunData data, int projectId)
protected Number
AbstractSimpleProjectTest. transformValue(Number value, RunData data)
Transform the value. -
Uses of RunData in fr.ens.biologie.genomique.aozan.tests.sample
Methods in fr.ens.biologie.genomique.aozan.tests.sample with parameters of type RunData Modifier and Type Method Description TestResult
AbstractFastQCSampleTest. test(RunData data, int read, int readSample, int sampleId)
TestResult
AbstractSimpleSampleTest. test(RunData data, int read, int readSample, int sampleId)
TestResult
BasePFMeanQualityScoreSampleTest. test(RunData data, int read, int readSample, int sampleId)
TestResult
ClusterRecoveryReportSampleTest. test(RunData data, int read, int readSample, int sampleId)
TestResult
FastQScreenReportSampleTest. test(RunData data, int read, int readSample, int sampleId)
TestResult
InLanePercentSampleTest. test(RunData data, int read, int readSample, int sampleId)
TestResult
PFPercentSampleTest. test(RunData data, int read, int readSample, int sampleId)
TestResult
Q30PercentSampleTest. test(RunData data, int read, int readSample, int sampleId)
TestResult
RecoverablePFClusterPercentSampleTest. test(RunData data, int read, int readSample, int sampleId)
TestResult
RecoverableRawClusterPercentSampleTest. test(RunData data, int read, int readSample, int sampleId)
TestResult
SampleTest. test(RunData data, int read, int readSample, int sampleId)
Do a test.protected int
AbstractSimpleSampleTest. transformScore(int score, RunData data, int read, int readSample, int sampleId)
Transform the score.protected int
FastQScreenMappedPercentSampleTest. transformScore(int score, RunData data, int read, int readSample, int sampleId)
Transform the score : if genome of sample is the same as reference genome.protected Number
AbstractSimpleSampleTest. transformValue(Number value, RunData data, int read, int readSample, int sampleId)
Transform the value.protected Number
FastQScreenMappedExceptRefGenomeSampleTest. transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
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Uses of RunData in fr.ens.biologie.genomique.aozan.util
Methods in fr.ens.biologie.genomique.aozan.util with parameters of type RunData Modifier and Type Method Description static void
XMLUtilsWriter. buildXMLCommonTagHeader(Document doc, Element parent, RunData data)
Add common tag in document header xml to describe Aozan and if data exists on run.
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