Class ReDemux
- java.lang.Object
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- fr.ens.biologie.genomique.aozan.demux.ReDemux
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public class ReDemux extends Object
This class allow to retrieve index from undetermined indices.- Author:
- Laurent Jourdren
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addIndex(int lane, String index)
Add an index to re-demultiplex.static void
main(String[] args)
static void
redemultiplex(File samplesheetFile, String bcl2fastqVersion, List<String> lanesAndIndex, File outputDir)
void
redmux()
Launch the re-demultiplexing.
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Method Detail
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addIndex
public void addIndex(int lane, String index) throws AozanException
Add an index to re-demultiplex.- Parameters:
lane
- the lane to re-demultiplexindex
- the index- Throws:
AozanException
- if the index is invalid
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redmux
public void redmux() throws IOException, fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException
Launch the re-demultiplexing.- Throws:
IOException
- if an IO error occurs while re-demultiplexingfr.ens.biologie.genomique.kenetre.bio.BadBioEntryException
- if an FASTQ entry read is invaldIOException
fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException
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redemultiplex
public static void redemultiplex(File samplesheetFile, String bcl2fastqVersion, List<String> lanesAndIndex, File outputDir) throws FileNotFoundException, IOException, AozanException, fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException
- Throws:
FileNotFoundException
IOException
AozanException
fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException
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main
public static void main(String[] args) throws FileNotFoundException, IOException, AozanException, fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException
- Throws:
FileNotFoundException
IOException
AozanException
fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException
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