Package org.snpeff

Class RegulationFileSplitBytType


  • public class RegulationFileSplitBytType
    extends java.lang.Object
    Split regulation files into smaller files (one per 'regulation type') Regulation files can be quite large and we cannot read them into memory. Also there might be thousands of different regulation types We read chunks of BLOCK_SIZE lines at a time to avoid running out of memory. Note that we cannot open one file descriptor per 'regulation type' and save each line into it, since we may also run out of file descriptors.
    Author:
    pcingola
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.util.Set<java.lang.String> getRegFileNames()  
      java.util.Collection<java.lang.String> getRegTypes()  
      void setVerbose​(boolean verbose)  
      void splitFile​(RegulationFileIterator regulationFileIterator, java.lang.String path)
      Read a regulation file and split into one file for each "regulation type"
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • RegulationFileSplitBytType

        public RegulationFileSplitBytType()
    • Method Detail

      • getRegFileNames

        public java.util.Set<java.lang.String> getRegFileNames()
      • getRegTypes

        public java.util.Collection<java.lang.String> getRegTypes()
      • setVerbose

        public void setVerbose​(boolean verbose)
      • splitFile

        public void splitFile​(RegulationFileIterator regulationFileIterator,
                              java.lang.String path)
        Read a regulation file and split into one file for each "regulation type"