Edited tophat.sh to use unfiltered bam in RNASeQC.
test generic header defaults
additional defaults refactored
Bugfix
Bugfix bam annotate file input
PICARD now ignores qualities for RNA-SeQC reordering.
Genome index task refactored
Bugfix.

Added missing brackets..
Bug fix missing brackets.
Bigwig Summary added
Bigwig Summary added
Bugfixes and smoketest updates
Merge branch 'master' into new_mods
Bugfix TASK anme
Merge branch 'new_mods' of github.com:clark-lab/ngsane into new_mods
Added some files to cleanup in tophat.sh
Bugfix dummy removal
Merge branch 'new_mods'
fix for unmapped reads
moved fix_tophat_unmapped_reads.pyto next checkpoint