Class BAMSplitter
- java.lang.Object
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- fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter
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Constructor Summary
Constructors Constructor Description BAMSplitter()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
configure(Set<Parameter> conf)
Configure the splitter.DataFormat
getFormat()
Get the format related to the splitter.void
split(DataFile inFile, Iterator<DataFile> outFileIterator)
Split data.void
splitByChromosomes(DataFile inFile, Iterator<DataFile> outFileIterator)
Split BAM file by chromosomes.
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Method Detail
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getFormat
public DataFormat getFormat()
Description copied from interface:Splitter
Get the format related to the splitter.
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configure
public void configure(Set<Parameter> conf) throws EoulsanException
Description copied from interface:Splitter
Configure the splitter.- Specified by:
configure
in interfaceSplitter
- Parameters:
conf
- configuration- Throws:
EoulsanException
- if the configuration is invalid
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split
public void split(DataFile inFile, Iterator<DataFile> outFileIterator) throws IOException
Description copied from interface:Splitter
Split data.- Specified by:
split
in interfaceSplitter
- Parameters:
inFile
- input DataFileoutFileIterator
- iterator over DataFile to create- Throws:
IOException
- if an error occurs while split data
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splitByChromosomes
public void splitByChromosomes(DataFile inFile, Iterator<DataFile> outFileIterator) throws IOException
Split BAM file by chromosomes.- Parameters:
inFile
- input fileoutFileIterator
- output files iterator- Throws:
IOException
- if an error occurs while reading or creating output files
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