Package picard.nio

Class PicardIOUtils

java.lang.Object
picard.nio.PicardIOUtils

public class PicardIOUtils extends Object
Ported from GATKIOUtils.java
  • Constructor Details

    • PicardIOUtils

      public PicardIOUtils()
  • Method Details

    • deleteOnExit

      public static void deleteOnExit(Path fileToDelete)
      Schedule a file or directory to be deleted on JVM shutdown. This calls deleteRecursively(Path) on fileToDelete as a shutdown hook.
      Parameters:
      fileToDelete - file or directory to be deleted recursively at JVM shutdown.
    • createTempFile

      public static File createTempFile(String name, String extension)
      Creates a temp file that will be deleted on exit This will also mark the corresponding Tribble/Tabix/BAM indices matching the temp file for deletion.
      Parameters:
      name - Prefix of the file; File.createTempFile(String, String, File) requires that this be >= 3 characters
      extension - Extension to concat to the end of the file.
      Returns:
      A file in the temporary directory starting with name, ending with extension, which will be deleted after the program exits.
    • createTempFileInDirectory

      public static File createTempFileInDirectory(String name, String extension, File targetDir)
      Creates a temp file in a target directory that will be deleted on exit This will also mark the corresponding Tribble/Tabix/BAM indices matching the temp file for deletion.
      Parameters:
      name - Prefix of the file; File.createTempFile(String, String, File) requires that this be >= 3 characters
      extension - Extension to concat to the end of the file name e.g. ".txt"
      targetDir - Directory in which to create the temp file. If null, the default temp directory is used.
      Returns:
      A file in the temporary directory starting with name, ending with extension, which will be deleted after the program exits. TODO: consolidate this and BucketUtils::getTempFilePath
    • deleteRecursively

      public static void deleteRecursively(Path rootPath)
      Delete rootPath recursively
      Parameters:
      rootPath - is the file/directory to be deleted