Allow types str and unicode for the value instance variable of Option objects to support file names.
In Analysis.run, support sample annotation sheet files in the same directory as the driver script is run.
Add support for the snpEff tool Java Archive (JAR), as well as the GATK and snpEff data directories.
Add support for data types str and unicode in methods setting Option objects via Command objects.
Reset parameter defaults for the Runnable.run method.
Added support for Java Archive (JAR) class paths for the GATK and snpEff tools, as well as data directories for the same tools.
Added support for the sequencing centre and moved from the process lanes to the sequences directory.
Moved the VariantCalling class from the crowded Bio.BSF.Analysis module into its own module.
Much of the code building up command lines has been moved back from bsf_run_variant_calling scripts into the VariantCalling library module.
More options are now configurable via the variant calling configuration file.
Added support for reads and index reads to the RunParameters class.
Extended the BSF Illumina Run Folder Summary script to also show the read structure and the start and end dates based on the modification times of the runParameters.xml and RTAComplete.txt files, respectively.