Adjusted code to also work with older versions of Illumina XML configuration files.
Added support for SAM ReadGroup (@RG) information to the PairedReads class.
Renamed Bash scripts to include their correct file suffix.
Propagate the SAM read group information around FASTQ files if required.
Further adjusted Java Virtual Machine memory requirements for GATK tools.
Added a utility script to convert a sequence dictionary in SAM file header format into UCSC chromosome sizes format.
Added a utility script to convert variant calls in VCF format into 23andMe format.
Moved RNA-Seq code from the Analyses module into a separate RNASeq module.