Uses of Class
fr.ens.biologie.genomique.aozan.AozanException
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Packages that use AozanException Package Description fr.ens.biologie.genomique.aozan Root package of Aozan.fr.ens.biologie.genomique.aozan.aozan3.legacy 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.demux This package allows to re-demultiplexing selected project sequencing.fr.ens.biologie.genomique.aozan.fastqc This package contains a QCModule for FastQC that list the bad tiles in a fastq file and class used for modify fastqc bytecode, it is necessary with FastQC version 0.10.1.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.tests This package contains class of tests which defines the collector to launch and creates a report of a quality control.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 AozanException in fr.ens.biologie.genomique.aozan
Methods in fr.ens.biologie.genomique.aozan that throw AozanException Modifier and Type Method Description RunData
RunDataGenerator. collect(QC qc)
Collect data and return a RunData object.QCReport
QC. computeReport()
Process data.String
QCReportExporter. export(File XSLFile)
Export the QC report.String
QCReportExporter. export(InputStream is)
Export the QC report.static void
Common. initLogger(String logPath)
Initialize the logger for the application.static void
Common. initLogger(String logPath, String logLevel)
Initialize the logger for the application.static void
Common. initLogger(String logPath, Level logLevel)
Initialize the logger for the application.Document
QCReport. toDocument()
Get Report as a XML Document.String
QCReportExporter. toXML()
Create the QC report as an XML String.void
QCReportExporter. writeRawData(File outputFile)
Write the raw data of the QC.void
QCReportExporter. writeRawData(String outputFilename)
Write the raw data of the QC.void
QCReportExporter. writeReport(InputStream xslIs, File outputFile)
Write the report usually in HTML) in a file.void
QCReportExporter. writeReport(String stylesheetFilename, String outputFilename)
Write the report usually in HTML) in a file.void
QCReportExporter. writeXMLReport(File outputFile)
Write the XML in a file.void
QCReportExporter. writeXMLReport(String outputFilename)
Write the XML in a file.Constructors in fr.ens.biologie.genomique.aozan that throw AozanException Constructor Description QC(Settings settings, String bclDir, String fastqDir, String qcDir, File tmpDir, String runId)
Public constructor.QC(Settings settings, String bclDir, String fastqDir, String qcDir, File tmpDir, String runId, fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet sampleSheet)
Public constructor.QC(Settings settings, String bclDir, String fastqDir, String qcDir, String tmpDirname, String runId)
Public constructor.QCReportExporter(QCReport qcReport)
Public constructor. -
Uses of AozanException in fr.ens.biologie.genomique.aozan.aozan3.legacy
Methods in fr.ens.biologie.genomique.aozan.aozan3.legacy that throw AozanException Modifier and Type Method Description static void
IndexGenerator. createIndexRun(Path outputDir, String runId, Collection<String> sections)
Create index.html file in legacy mode. -
Uses of AozanException in fr.ens.biologie.genomique.aozan.collectors
Methods in fr.ens.biologie.genomique.aozan.collectors that throw AozanException 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
SubsetFastqThread. process()
protected void
UndeterminedIndexesProcessThread. process()
protected void
UndeterminedIndexesProcessThread. processResults()
Process results after the end of the thread.Constructors in fr.ens.biologie.genomique.aozan.collectors that throw AozanException 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 AozanException in fr.ens.biologie.genomique.aozan.collectors.interop
Methods in fr.ens.biologie.genomique.aozan.collectors.interop that throw AozanException 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 AozanException in fr.ens.biologie.genomique.aozan.collectors.stats
Methods in fr.ens.biologie.genomique.aozan.collectors.stats that throw AozanException Modifier and Type Method Description void
EntityStat. addEntity(int sampleId)
Adds the sample.void
EntityStat. addRunDataProjectEntries(String prefix)
Creates the run data project.Map<Integer,EntityStat>
ProjectStatisticsCollector. extractEntityStats(RunData data)
Map<Integer,EntityStat>
SampleStatisticsCollector. extractEntityStats(RunData data)
Constructors in fr.ens.biologie.genomique.aozan.collectors.stats that throw AozanException 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 AozanException in fr.ens.biologie.genomique.aozan.demux
Methods in fr.ens.biologie.genomique.aozan.demux that throw AozanException Modifier and Type Method Description void
ReDemux. addIndex(int lane, String index)
Add an index to re-demultiplex.static void
ReDemux. main(String[] args)
static void
ReDemux. redemultiplex(File samplesheetFile, String bcl2fastqVersion, List<String> lanesAndIndex, File outputDir)
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Uses of AozanException in fr.ens.biologie.genomique.aozan.fastqc
Methods in fr.ens.biologie.genomique.aozan.fastqc that throw AozanException Modifier and Type Method Description fr.ens.biologie.genomique.aozan.fastqc.BlastResultHit
OverrepresentedSequencesBlast. getResult(String sequence)
Get the blast result of a sequencestatic void
RuntimePatchFastQC. runPatchFastQC()
Execute method who patch code from FastQC before call in Aozan.static void
RuntimePatchFastQC. runPatchFastQC(boolean useBlast)
Execute method who patch code from FastQC before call in Aozan. -
Uses of AozanException in fr.ens.biologie.genomique.aozan.fastqscreen
Methods in fr.ens.biologie.genomique.aozan.fastqscreen that throw AozanException Modifier and Type Method Description void
FastqScreenResult. countPercentValue(int readsMapped, int readsprocessed)
Convert values from fastqscreen in percentage.void
FastqScreenProjectReport. createReport(File reportHtml)
Creates the HTML report.RunData
FastqScreenResult. createRundata(String prefix)
Update rundata with results from fastqscreen.void
FastqScreenPseudoMapReduce. doMap(File fastqRead1, File fastqRead2, List<String> genomes, String sampleGenome, int threadNumber)
Mapper Receive value in SAM format, only the read mapped are added in output with reference genome.void
FastqScreenPseudoMapReduce. doMap(File fastqRead, List<String> genomes, String sampleGenome, int threadNumber)
Mapper Receive value in SAM format, only the read mapped are added in output with reference genome.FastqScreenResult
FastqScreen. execute(File fastqRead1, File fastqRead2, String sampleDescription, List<String> genomes, String sampleGenome, boolean isPairedMode)
Mode single-end : execute fastqscreen.FastqScreenResult
FastqScreen. execute(File fastqRead, String sampleDescription, List<String> genomes, String genomeSample, boolean paired)
Mode pair-end : execute fastqscreen.FastqScreenGenomes
FastqScreen. getFastqScreenGenomes()
FastqScreenResult
FastqScreenPseudoMapReduce. getFastqScreenResult()
Compile data of fastqscreen in percentage.static GenomeAliases
GenomeAliases. getInstance()
Create a instance of GenomeAliases or if it exists return instance.static void
GenomeAliases. initialize(Settings settings)
Create a instance of GenomeAliases or if it exists return instance.static FastqScreenGenomes
FastqScreenGenomes. newInstance(TestConfiguration testConfiguration)
Private constructor of FastqScreenGenomeMapper.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.Constructors in fr.ens.biologie.genomique.aozan.fastqscreen that throw AozanException Constructor Description FastqScreenGenomes(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet, String contaminantGenomeNames)
Public constructor.FastqScreenPseudoMapReduce(File tmpDir, boolean pairedMode, String mapperName, String mapperArguments)
Public construction. -
Uses of AozanException in fr.ens.biologie.genomique.aozan.tests
Methods in fr.ens.biologie.genomique.aozan.tests that throw AozanException Modifier and Type Method Description List<AozanTest>
AozanTest. configure(TestConfiguration conf)
Configure the test.void
AozanTest. init()
Initialize the test. -
Uses of AozanException in fr.ens.biologie.genomique.aozan.tests.global
Methods in fr.ens.biologie.genomique.aozan.tests.global that throw AozanException Modifier and Type Method Description List<AozanTest>
AbstractSimpleGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
ClusterDensityGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
ClusterDensityPFGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
ErrorRateGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
OccupancyPercentGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
ProjectCountGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
Q30PercentGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
SampleCountGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
UndeterminedClusterPercentGlobalTest. configure(TestConfiguration conf)
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Uses of AozanException in fr.ens.biologie.genomique.aozan.tests.lane
Methods in fr.ens.biologie.genomique.aozan.tests.lane that throw AozanException Modifier and Type Method Description List<AozanTest>
AbstractSimpleLaneTest. configure(TestConfiguration conf)
List<AozanTest>
PFClusterPercentLaneTest. configure(TestConfiguration conf)
List<AozanTest>
PhasingPrephasingPercentLaneTest. configure(TestConfiguration conf)
List<AozanTest>
PhiXAlignPercentLaneTest. configure(TestConfiguration oonf)
List<AozanTest>
PhiXRawClusterCountLaneTest. configure(TestConfiguration conf)
List<AozanTest>
Q30PercentLaneTest. configure(TestConfiguration conf)
List<AozanTest>
YieldLaneTest. configure(TestConfiguration conf)
List<AozanTest>
YieldPFLaneTest. configure(TestConfiguration conf)
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Uses of AozanException in fr.ens.biologie.genomique.aozan.tests.pooledsample
Methods in fr.ens.biologie.genomique.aozan.tests.pooledsample that throw AozanException Modifier and Type Method Description List<AozanTest>
AbstractSimpleSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQScreenMappedPercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQScreenReportPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQScreenSampleOvercontaminationCountPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
InProjectPercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
InRunPercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
PFBaseMeanQualityScorePooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
PFPercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
Q30PercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
RecoverablePFClusterPercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
RecoverableRawClusterPercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
SampleInPoolCountPooledSampleTest. configure(TestConfiguration conf)
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Uses of AozanException in fr.ens.biologie.genomique.aozan.tests.project
Methods in fr.ens.biologie.genomique.aozan.tests.project that throw AozanException Modifier and Type Method Description List<AozanTest>
AbstractSimpleProjectTest. configure(TestConfiguration conf)
List<AozanTest>
FastQScreenReportProjectTest. configure(TestConfiguration conf)
List<AozanTest>
MultiQCReportProjectTest. configure(TestConfiguration conf)
List<AozanTest>
RecoverablePFClusterPercentProjectTest. configure(TestConfiguration conf)
List<AozanTest>
RecoverableRawClusterPercentProjectTest. configure(TestConfiguration conf)
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Uses of AozanException in fr.ens.biologie.genomique.aozan.tests.sample
Methods in fr.ens.biologie.genomique.aozan.tests.sample that throw AozanException Modifier and Type Method Description List<AozanTest>
AbstractSimpleSampleTest. configure(TestConfiguration conf)
List<AozanTest>
BasePFMeanQualityScoreSampleTest. configure(TestConfiguration conf)
List<AozanTest>
ClusterRecoveryReportSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCAdapterContentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCBasicStatsSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCDuplicationLevelSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCKmerContentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCNContentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCOverrepresentedSequencesSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCPerBaseQualityScoresSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCPerBaseSequenceContentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCPerSequenceGCContentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCPerSequenceQualityScoresSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCPerTileSequenceQualitySampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCSequenceLengthDistributionSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQScreenMappedPercentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQScreenReportSampleTest. configure(TestConfiguration conf)
List<AozanTest>
InLanePercentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
PFPercentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
Q30PercentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
RecoverablePFClusterPercentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
RecoverableRawClusterPercentSampleTest. configure(TestConfiguration conf)
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Uses of AozanException in fr.ens.biologie.genomique.aozan.util
Methods in fr.ens.biologie.genomique.aozan.util that throw AozanException 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.void
ScoreInterval. configureDoubleInterval(TestConfiguration conf)
boolean
ScoreInterval. configureDoubleInterval(String key, String value)
boolean
ScoreInterval. configureLongInterval(String key, String value)
void
ScoreInterval. configureLongInterval(Map<String,String> properties)
static String
XMLUtilsWriter. createHTMLFileFromXSL(File XMLFile, File XSLFile)
Transform a XML file using XSL style sheet.static String
XMLUtilsWriter. createHTMLFileFromXSL(String XMLPath, String XSLPath)
Transform a XML file using XSL style sheet.static String
XMLUtilsWriter. createHTMLFileFromXSL(Document doc, InputStream isXslFile)
Create a html file from document xml and xsl files.static void
XMLUtilsWriter. createHTMLFileFromXSL(Document doc, InputStream isXslFile, File reportHtml)
Create a html file from document xml and xsl files.static void
XMLUtilsWriter. createXMLFile(Document doc, File output)
Create a xml file from document xml.static String
XMLUtilsWriter. createXMLFileContent(Document doc)
Create a XML file content from XML document.Constructors in fr.ens.biologie.genomique.aozan.util that throw AozanException Constructor Description DoubleInterval(String s)
LongInterval(String s)
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