Changed Python docstrings to use Epytext annotation rather than reStructuredText.
Corrected the syntax in type fields, where types are now separated by pipe characters.
Removed empty lines after function definitions.
Changed Python docstrings to use Epytext annotation rather than reStructuredText.
Corrected the syntax in type fields, where types are now separated by pipe characters.
Removed empty lines after function definitions.
Changed Python docstrings to use Epytext annotation rather than reStructuredText.
Corrected the syntax in type fields, where types are now separated by pipe characters.
Removed empty lines after function definitions.
Added a gitignore file to exclude compiled Python code (pyc) files.
In class Command fixed the methods setting (i.e. overriding) Argument objects to really use the set_argument method.
Changed Python docstrings to use Epytext annotation rather than reStructuredText.
Corrected the syntax in type fields, where types are now separated by pipe characters.
Removed empty lines after function definitions.
Changed Python docstrings to use Epytext annotation rather than reStructuredText.
Corrected the syntax in type fields, where types are now separated by pipe characters.
Removed empty lines after function definitions.
The os.path.basename method does not accept named arguments.
Standardised the definition of Python argparse option entries.
Adjusted the BamIndexDecoder configuration template to the new code modules.
Adjusted the IlluminaToBam configuration template to the new code modules.
Updated the custom dictionary for the spell checker.
Changed project settings to use the Epytext documentation style.
Removed the old IlluminaToBam-Tools infrastructure.
Moved the ChIP-Seq code from the Analysis module into a separate ChIPSeq module.
Added a driver script for the new ChIPSeq analysis.
Commented out code to fetch all ProcessSLURM objects by a job name.
Removed the Collection.read_SampleAnnotationSheet method and implemented its functionality directly in Collection.from_sas.
Added AnnotationSheet class variables that provide defaults for the initialisation of instance variables that store options required for csv.DictReader and csv.DictWriter instantiation.
These AnnotationSheet class variables can be overridden in sub-classes to provide specific defaults such ass field names.
Changed AnnotationSheet class variable names around regular expression.
Removed the now redundant AnnotationSheet.read_tsv method, as tab-separated value files can be read by setting the file_type instance variable to 'excel-tab'.
Removed sub-class methods BamIndexDecoderSheet.read_from_file, BamIndexDecoderSheet.__init__, SampleAnnotationSheet.read_from_file and SampleAnnotationSheet.__init__.
Added a new class TuxedoSamplePairSheet to read sample pair information of a Cuffdiff time series defined by the bsf_rnaseq_process_cuffdiff.R script.
Moved paths for the genome sequence FASTA file and the transcriptome GTF file into instance variables.
Changed the bsf_rnaseq_process_cuffdiff.R script option 'comparison' to 'comparison-name',  'genome_directory' to 'genome-directory' and added options 'gtf-file' and 'genome-version'.
Updated the RNASeq.report method to changes applied to the bsf_rnaseq_process_cuffdiff.R, most importantly, the splitting of data frames and addition of QC plots for each sample pair in a time series.
Adjustments to changes in the AnnotationSheet class.