Package htsjdk.beta.plugin

Class IOUtils

java.lang.Object
htsjdk.beta.plugin.IOUtils
public class IOUtils extends Object
Class for updated IOUtils methods that use either IOPath Path in public method argument lists.

  • Constructor Details

    • IOUtils

      public IOUtils()

  • Method Details

    • createTempPath

      public static IOPath createTempPath(String prefix, String suffix)
      Create a temporary file using a given name prefix and name suffix and return a Path.
      Parameters:
      prefix -
      suffix -
      Returns:
      temp File that will be deleted on exit
      Throws:
      IOException

    • toHtsPath

      public static HtsPath toHtsPath(Path toConvert)
      Convert Path to GATKPath, returning null if input was null.
      Parameters:
      toConvert - Path to convert to GATKPath
      Returns:
      a Path, or null if the input was null.

    • getStringFromPath

      public static String getStringFromPath(IOPath ioPath)
      Get the entire contents of an IOPath as a string.
      Parameters:
      ioPath -
      Returns:
      a UTF-8 string representation of the file contents

    • writeStringToPath

      public static void writeStringToPath(IOPath ioPath, String contents, boolean gzipOutput)
      Write a String to an IOPath.
      Parameters:
      ioPath - path where contents should be written
      contents - a UTF-8 string to be written
      gzipOutput - if true, gzip output