GATKvariant calling sample config
Checking software tool availability before starting job
test if programs are available before starting calculation
rm $OUTDIR/mask.gff
Added RNA-SeQC

RNA-SeQC runs per sample in tophatcuff.sh
bugfix hiclib corrleation

parameter passing adjusted
bugfix log printing
save multiple hiclib figures in one plot
Modified CalcGencodeGeneRPKM

Provide gene level RPKMs for Gencode genes using edgeR.
single dataset plot rearranged
bugfix
add hiclib correlation analysis as postcommand
Added ht-seqcount for cufflinks gtf (gencode guided)
postonly step annotated in trigger
hiclib correlation streamlined
figure size specified
bugfix figure generation
separate qsub parameter specification for postcommand

allows to specify a separate parameter set for postcommands (i.e. cpus,
nodes, memory and walltime)
Bugfix hiclib image generation
Bugfix parameter handling for postcommand jobs