Package fr.ens.biologie.genomique.eoulsan.splitermergers

Class SAMSplitter

java.lang.Object
fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter
All Implemented Interfaces:
Splitter
public class SAMSplitter extends Object implements Splitter
This class define a splitter class for SAM files.
Since:
2.0
Author:
Laurent Jourdren

  • Constructor Details

    • SAMSplitter

      public SAMSplitter()

  • Method Details

    • getFormat

      public DataFormat getFormat()
      Description copied from interface: Splitter
      Get the format related to the splitter.
      Specified by:
      getFormat in interface Splitter
      Returns:
      a DataFormat object

    • configure

      public void configure(Set<Parameter> conf) throws EoulsanException
      Description copied from interface: Splitter
      Configure the splitter.
      Specified by:
      configure in interface Splitter
      Parameters:
      conf - configuration
      Throws:
      EoulsanException - if the configuration is invalid

    • split

      public void split(DataFile inFile, Iterator<DataFile> outFileIterator) throws IOException
      Description copied from interface: Splitter
      Split data.
      Specified by:
      split in interface Splitter
      Parameters:
      inFile - input DataFile
      outFileIterator - iterator over DataFile to create
      Throws:
      IOException - if an error occurs while split data

    • splitByChromosomes

      public void splitByChromosomes(DataFile inFile, Iterator<DataFile> outFileIterator) throws IOException
      Split SAM file by chromosomes.
      Parameters:
      inFile - input file
      outFileIterator - output files iterator
      Throws:
      IOException - if an error occurs while reading or creating output files