Appends text to file.
Appends text to file. Opens a new java.io.FileWriter on every call.
Appends text to file.
Appends text to file. Opens a new java.io.FileWriter on every call.
Concatenates text files together, dropping header lines for each, except the first.
Returns a scala.io.Source from the given GZipped file.
Execute command with user function to process each line of output.
Execute command with user function to process each line of output.
Based on from http://www.jroller.com/thebugslayer/entry/executing_external_system_commands_in Creates 3 new threads: one for the stdout, one for the stderror, and one waits for the exit code.
Description of the executable process
Maximum time to wait for the process to complete. Default infinite.
Exit code of the process.
Execute command.
Execute command. Returns stdout and stderr as strings, and true if it was successful.
A process is considered successful if its exit code is 0 and the error stream is empty. The latter criterion can be disabled with the unsuccessfulOnErrorStream parameter.
The process description.
if true, then the process is considered as a failure if its stderr is not empty.
max waiting time.
(stdout,stderr,success) triples
Execute command.
Execute command. Returns stdout and stderr as strings, and true if it was successful. Also writes to log.
A process is considered successful if its exit code is 0 and the error stream is empty. The latter criterion can be disabled with the unsuccessfulOnErrorStream parameter.
The process description.
if true, then the process is considered as a failure if its stderr is not empty.
max waiting time.
A logger.
(stdout,stderr,success) triples
Returns true if file is empty.
Returns a java.io.BufferedReader.
Returns a java.io.BufferedWriter.
Returns true if the file is GZipped.
Returns true if the file is GZipped.
Opens a buffered java.io.BufferedInputStream on the file.
Opens a buffered java.io.BufferedInputStream on the file. Closes it after the block is executed.
Opens a buffered java.io.BufferedOutputStream on the file.
Opens a buffered java.io.BufferedOutputStream on the file. Closes it after the block is executed.
Opens a buffered java.io.BufferedReader on the file.
Opens a buffered java.io.BufferedReader on the file. Closes it after the block is executed.
Opens a java.io.BufferedWriter on the file.
Opens a java.io.BufferedWriter on the file. Closes it after the block is executed.
Opens a scala.io.Source, executes the block, then closes the source.
Opens a scala.io.Source, executes the block, then closes the source.
Path of the file
Opens a scala.io.Source, executes the block, then closes the source.
Opens a scala.io.Source, executes the block, then closes the source.
Path of the file
Opens an unbuffered java.io.Writer on the file.
Opens an unbuffered java.io.Writer on the file. Closes it after the block is executed.
Opens a java.io.OutputStream which writes GZip compressed data to the given path.
Opens a java.io.OutputStream which writes GZip compressed data to the given path. Closes it after the block is executed.
Opens a java.io.OutputStream which writes GZip compressed data to the given path.
Opens a java.io.OutputStream which writes GZip compressed data to the given path. Closes it after the block is executed.
Opens a java.io.BufferedReader on a GZipped file.
Opens a java.io.BufferedReader on a GZipped file. Closes it after the block is executed.
Opens a java.io.BufferedWriter which writes GZip compressed data to the given path.
Opens a java.io.BufferedWriter which writes GZip compressed data to the given path. Closes it after the block is executed.
Creates symbolic links with the same basename but different extensions.
Creates symbolic links with the same basename but different extensions.
files with the needed extensions
A temporary File which points to the common part of the symbolic links paths.
Reads file contents into a bytearray.
Reads file contents into a bytearray.
Reads file contents into a bytearray.
Returns an iterator on the InputStream's data.
Returns an iterator on the InputStream's data.
Closes the stream when read through.
Searches $PATH for the specified file
Returns the result of the block, and closes the resource.
Returns the result of the block, and closes the resource.
closeable resource
block using the resource
Alias for useResource
Writes binary data to file.
Writes binary data to file.
Writes the ByteBuffer's contents to a file.
Writes the ByteBuffer's contents to a file.
Writes text data to file.
Writes text data to file.
Provides classes and methods for general bionformatic applications.