made ONEKGVCF optional
bug in recalirbration script and sampleConfig
Minor bugfix.

/share/ClusterShare/software/contrib/hugfre/ngsane//mods/tophat.sh:
line 130: [_R1: command not found
Forced sorting for BAM to be properly ordered for RNA-SeQC
Added transcript gencode calc to htseqcount.sh + bugfix

removed .bam as samtools gives this prefix in tophat.sh
Added index for RNA-SeQC bam.
Modified HTSeq type.

Edited unique read selection to include.
added setup script
added install script
changed project card image
Bugfix Samplepattern parsing
Merge branch 'master' of github.com:clark-lab/ngsane
delete dummy files when finished
expected Tophat results adjusted
Garvan reference location for Gencode adjusted
Merge remote-tracking branch 'allpower/master'
Merge branch 'master' into masai_fseq