Added support for custom tranche filtering at the GATK ApplyRecalibration stage.
Added two further steps to the GATK pipeline to split the multi-sample VCF into sample-specific ones via SelectVariants and converted the sample-specific VCFs into tab-delimited text via VariantsToTable.
Added the name of a resource to the corresponding parameter of the VariantRecalibrator in the run method.
Removed the trailing dot from the regular expression for Picard MarkDuplicates.
Added support for time limits in the Default and DRMS classes.
Introduced a new DRMS:set_Default method to formalise setting of Defaults for class methods instantiating a DRMS object.
In DatabaseAdaptor.create_tables check in the sqlite_master table whether a particular table already exists.
Added documentation.
Added preliminary support for a SQLite database and optimised some sbatch options.
Added a script to convert Picard sequence dictionary files based on the SAM format into UCSC chromosome sizes files.
Added a script to convert a VCF file into a 23andMe file.
Adjusted the Java heap size (Xmx) for the GATK IndelRealigner step to 6 GiB.
In method picard_sam_to_fastq, adjusted the DRMS.name values to all lower case for consistency.
Added another parameter to DRMS.set_Configuration to allow suppression of warnings about missing sections in the configuration file.
Improved the code documentation by adding return value information.
Allow skipping of the Picard MarkDuplicates step in the VariantCallingGATK.run method via a new configuration option.
Allow skipping of the Picard MarkDuplicates step.
Activated automatic deletion of intermediate files.
Optimised code around warnings and exceptions.
Changed the extension of Bash scripts from *.sh to *.bash.
Reformatted the code.
Optimised code around warnings and exceptions.
Replaced string.format() with string.join() methods where they should be more efficient.
Added support for a standard DRMS time limit.
Adjusted the analysis templates.
Optimised code around warnings and exceptions.