Fixed the logic of the force parameter, required that the output directory exists and extended the search pattern for Picard *_barcode.txt files to also include *_barcode.txt.gz files.
Modified BSF AnnotationSheet class methods to allow checking for sequence checking in mandatory or optional mode.
Increased the Java Virtual Machine memory requirements for the Picard SortSam step to 6 GiB.
Added a log message after the end of file (EOF) mark has been encountered while reading from the STDOUT and STDERR pipes.
Added a class for the Burrows Wheeler Aligner (BWA) version 0.7 and above.
Corrected the Reads1 information in sample annotation sheets after BamIndexDecoder de-multiplexing. The reads have to be unique, so the flow cell identifier and the lane needed including.
Fixed the Bio.BSF.Command.trace method that did not pass on the output of the trace for the sub_command object.
Added trace methods
Reformatted code
In Command.trace add tracing of Option objects
Reformatted code
Allow Command objects with empty command instance variables so that Command objects can be used to structure OptionPair objects after Executable Option objects.
Renamed command variables in the command_list() and command_str() methods into command_line to avoid ambiguities.
Fixed a bug where Thread.is_alive() was called as an instance variable rather than a method, so that Threads never seemed to exit.
Renamed variables threading_timeout and max_threads.
Introduced weak references into the data object hierarchy to allow linking back from e.g. Sample to Project objects.
Pipes should definitely not be closed from within the output processing threads.
Changed the instance variables stdout and stderr to stdout_path and stderr_path for better code readability and moved the STDOUT and STDERR redirection to the specific modules Bio.BSF.DRMS.Bash and Bio.BSF.DRMS.SGE.
Renamed the Bio.BSF.Runnable modules into Bio.BSF.Runnables in preparation for a new class.
Introduced a new class Bio.BSF.Runnable to wrap the Python subprocess module.
Renamed the Bio.BSF.Executable.BWA07 class into Bio.BSF.Executable.BWA.
Added instance variable classpath_gatk to the Bio.BSF.Default class.
Changed the representation of Command.options from a Python dict of Bio.BSF.Argument.Argument objects to a Python dict of Python list objects to support programs that take the same option multiple times.
Added support for the Simple Linux Utility for Resource Management (SLURM).
Added support for SQLite databases.
Initial attempt at a new variant calling pipeline.