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UPDATE: Update the IBENS genomic platform tool website URL from tools.genomique.biologie.ens.fr to outils.genomique.biologie.ens.fr.
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Diff for: ‎checkstyle-license.txt

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* For more information on the Aozan project and its aims,
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* or to join the Aozan Google group, visit the home page at:
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*
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* http://tools.genomique.biologie.ens.fr/aozan
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* http://outils.genomique.biologie.ens.fr/aozan
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*
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*/

Diff for: ‎generate-bcl2fastq-samplesheet-validator.sh

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@@ -71,7 +71,7 @@ The CASAVA/bcl2fastq version 1.8 sample sheet validator helps users to check the
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This tool generates a sample sheet only in csv format with a very strict syntax.
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It ensures you that the demultiplexing will not fail because the sample sheet is no correct.
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You can use the validator in association with Aozan, a tool that automatically handles data transfer, demultiplexing conversion and quality control once a HiSeq run is over (developed by Genomic Paris Centre and available at http://tools.genomique.biologie.ens.fr/aozan/).
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You can use the validator in association with Aozan, a tool that automatically handles data transfer, demultiplexing conversion and quality control once a HiSeq run is over (developed by Genomic Paris Centre and available at http://outils.genomique.biologie.ens.fr/aozan/).
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The validator is very simple to use:
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1/ copy the sample sheet from your spreadsheet or csv/tsv format in the first tab with the column headers;
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<h4 align="right">__VERSION__</h4>
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<div>
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<a href="https://www.genomique.biologie.ens.fr" ><img src="http://tools.genomique.biologie.ens.fr/aozan/images/logo_genomicpariscentre-90pxh.png" alt="logo genomic paris centre" align="left"/></a>
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<a href="https://www.genomique.biologie.ens.fr" ><img src="http://outils.genomique.biologie.ens.fr/aozan/images/logo_genomicpariscentre-90pxh.png" alt="logo genomic paris centre" align="left"/></a>
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<h1>CASAVA/BCL2FASTQ version 1.8 samplesheet validator</h1>
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</div>
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<table align="center">

Diff for: ‎src/main/java/files/aozan.xsl

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<div class="header">
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<div id="header_title">
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<span><img src="http://tools.genomique.biologie.ens.fr/aozan/images/logo_aozan_qc.png" alt="Aozan"/></span>
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<span><img src="http://outils.genomique.biologie.ens.fr/aozan/images/logo_aozan_qc.png" alt="Aozan"/></span>
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<span>Quality report on run <xsl:value-of select="/QCReport/RunId"/></span>
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</div>
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Diff for: ‎src/main/java/files/fastqscreen.xsl

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<body>
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<div class="header">
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<div id="header_title">
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<img src="http://tools.genomique.biologie.ens.fr/aozan/images/logo_aozan_qc.png" alt="Aozan"/>
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<img src="http://outils.genomique.biologie.ens.fr/aozan/images/logo_aozan_qc.png" alt="Aozan"/>
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Detection contamination report
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</div>
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</div>
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<xsl:value-of select="/ReportFastqScreen/Report/ReadsProcessed/@name"/> </li>
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</ul>
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<p><a href="http://tools.genomique.biologie.ens.fr/aozan/qc-samples-tests.html#contamination" target="_blank">Contamination detection detail report</a></p>
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<p><a href="http://outils.genomique.biologie.ens.fr/aozan/qc-samples-tests.html#contamination" target="_blank">Contamination detection detail report</a></p>
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<p>-</p>
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</div>
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Diff for: ‎src/main/java/files/fastqscreen_project.xsl

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<body>
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<div class="header">
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<div id="header_title">
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<img src="http://tools.genomique.biologie.ens.fr/aozan/images/logo_aozan_qc.png" alt="Aozan"/>
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<img src="http://outils.genomique.biologie.ens.fr/aozan/images/logo_aozan_qc.png" alt="Aozan"/>
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Detection contamination report for project <b><xsl:value-of select="/ReportFastqScreen/projectName"/></b>
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</div>
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</div>

Diff for: ‎src/main/java/files/template_index_run.html

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<div class="header">
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<div id="header_title">
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<img src="http://tools.genomique.biologie.ens.fr/aozan/images/logo_aozan_qc.png" alt="Aozan" />&#xA0;&#xA0;
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<img src="http://outils.genomique.biologie.ens.fr/aozan/images/logo_aozan_qc.png" alt="Aozan" />&#xA0;&#xA0;
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Run ${RUN_ID} reports</div>
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</div>
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Diff for: ‎src/main/java/files/undetermined_report.xsl

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<div class="header">
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<div id="header_title">
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<img
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src="http://tools.genomique.biologie.ens.fr/aozan/images/logo_aozan_qc.png"
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src="http://outils.genomique.biologie.ens.fr/aozan/images/logo_aozan_qc.png"
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alt="Aozan" />
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Clusters recoverable in
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<xsl:value-of select="/RecoveryClusterReport/sampleName" />

Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/AozanException.java

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* For more information on the Aozan project and its aims,
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* or to join the Aozan Google group, visit the home page at:
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*
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* http://tools.genomique.biologie.ens.fr/aozan
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* http://outils.genomique.biologie.ens.fr/aozan
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*
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/AozanRuntimeException.java

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* For more information on the Aozan project and its aims,
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* or to join the Aozan Google group, visit the home page at:
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*
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* http://tools.genomique.biologie.ens.fr/aozan
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* http://outils.genomique.biologie.ens.fr/aozan
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*
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/Common.java

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* For more information on the Aozan project and its aims,
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* or to join the Aozan Google group, visit the home page at:
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*
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* http://tools.genomique.biologie.ens.fr/aozan
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* http://outils.genomique.biologie.ens.fr/aozan
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*
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/Globals.java

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* For more information on the Aozan project and its aims,
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* or to join the Aozan Google group, visit the home page at:
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*
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* http://tools.genomique.biologie.ens.fr/aozan
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* http://outils.genomique.biologie.ens.fr/aozan
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*
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/QC.java

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* For more information on the Aozan project and its aims,
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* or to join the Aozan Google group, visit the home page at:
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*
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* http://tools.genomique.biologie.ens.fr/aozan
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* http://outils.genomique.biologie.ens.fr/aozan
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*
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/QCReport.java

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* For more information on the Aozan project and its aims,
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* or to join the Aozan Google group, visit the home page at:
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* http://tools.genomique.biologie.ens.fr/aozan
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* http://outils.genomique.biologie.ens.fr/aozan
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/RunData.java

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* For more information on the Aozan project and its aims,
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* or to join the Aozan Google group, visit the home page at:
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* http://outils.genomique.biologie.ens.fr/aozan
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*
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/RunDataGenerator.java

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* or to join the Aozan Google group, visit the home page at:
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* http://outils.genomique.biologie.ens.fr/aozan
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/Settings.java

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* For more information on the Aozan project and its aims,
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* http://tools.genomique.biologie.ens.fr/aozan
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* http://outils.genomique.biologie.ens.fr/aozan
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/AbstractFastqCollector.java

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* For more information on the Aozan project and its aims,
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* or to join the Aozan Google group, visit the home page at:
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* http://outils.genomique.biologie.ens.fr/aozan
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/AbstractFastqProcessThread.java

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* For more information on the Aozan project and its aims,
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* or to join the Aozan Google group, visit the home page at:
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* http://outils.genomique.biologie.ens.fr/aozan
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/AozanCollector.java

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* For more information on the Aozan project and its aims,
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package fr.ens.biologie.genomique.aozan.collectors;

Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/Collector.java

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* http://outils.genomique.biologie.ens.fr/aozan
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/CollectorRegistry.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/ConversionStatsCollector.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/DemultiplexingCollector.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/DesignCollector.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/FastQCCollector.java

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* For more information on the Aozan project and its aims,
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/FastQCProcessThread.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/FastqScreenCollector.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/FastqScreenProcessThread.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/FlowcellDemuxSummaryCollector.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/GlobalStatsCollector.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/PhasingCollector.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/ReadCollector.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/ReadXMLCollector.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/RunInfoCollector.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/StatisticsCollector.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/SubsetFastqCollector.java

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* or to join the Aozan Google group, visit the home page
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* at:
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* http://outils.genomique.biologie.ens.fr/aozan
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*
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*/
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/SubsetFastqThread.java

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* or to join the Aozan Google group, visit the home page
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* http://outils.genomique.biologie.ens.fr/aozan
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*
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*/
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/UndeterminedIndexesCollector.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/UndeterminedIndexesProcessThread.java

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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/interop/AbstractBinaryFileReader.java

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* For more information on the Aozan project and its aims,
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* or to join the Aozan Google group, visit the home page at:
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*
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* http://tools.genomique.biologie.ens.fr/aozan
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* http://outils.genomique.biologie.ens.fr/aozan
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*
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/interop/AbstractMetricsCollector.java

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* For more information on the Aozan project and its aims,
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* or to join the Aozan Google group, visit the home page at:
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*
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* http://tools.genomique.biologie.ens.fr/aozan
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* http://outils.genomique.biologie.ens.fr/aozan
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*
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*/
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Diff for: ‎src/main/java/fr/ens/biologie/genomique/aozan/collectors/interop/ErrorMetricsCollector.java

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* For more information on the Aozan project and its aims,
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* or to join the Aozan Google group, visit the home page at:
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*
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* http://tools.genomique.biologie.ens.fr/aozan
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* http://outils.genomique.biologie.ens.fr/aozan
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*
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*/
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