In Analysis.set_Configuration and DRMS.set_Configuration raise an Exception if the section does not exist, rather than just issue a UserWarning.
Since the Pickler cannot serialise weak references, which are part of classes defined in the Data module and referenced by Analysis objects, the pickling of data structures had to be moved from the Analysis to the Runnable class.
Introduce new functions to set (i.e. override) and not just add to Command options.
In Analysis.run, automatically create new analysis project and genome sub-directories, as long as the output directory exists.
Fix Analysis.create_public_project_link to use the html_path directory as the base for relative symbolic links.
In the Default class, introduce a new class variable to hold the file path to the bsfpython.ini file after user and variable expansion, in preparation for global Analysis configuration in this file.
The AnnotationSheet.validate method now uses a Python dict of column name key data and Python list value data of test method pointers. Several test methods can now be applied for each column.
Further class methods have been added to find leading, trailing or multiple adjacent underscore characters.
Improved the validation of BamIndexDecoderSheet objects via improvements to the AnnotationSheet class in addition to further tests for consistent barcode sequence lengths and sequence availability.
BamIndexDecoderSheet.validate now accepts a parameter specifying the number of lanes to validate in lieu of Illumina HiSeq 2500 rapid run flow-cells with only two lanes.
Brought the BSF SampleAnnotationSheet class to life.
Introduced global configuration for the BSF IlluminaToBam and BamIndexDecoder analyses.
Fixed some typos
Adjustments to changes in the AnnotationSheet class.
Rename functions to all lower case characters.
Adjustments to changes in the AnnotationSheet class.
Adjustments to changes in the AnnotationSheet class.
Rename functions to all lower case characters.
Modified the IlluminaToBamTools package to allow for non-redundant, global configuration files and chaining of IlluminaToBam and BamIndexDecoder analyses via project directories.