Remove trailing whitespace.
Add option to keep header in bed/vcf file
Add -v intersect type
Remove trailing tabs introduced by intersectBed
Merge branch 'updated' into gb_master
bug fixed
Merge branch 'master' of ssh://git/srv/git/genome
set config to test config
updated test data version and REBUILD because new instrument data came through
added the ability to specify base quality
Merge branch 'master' of ssh://git/srv/git/genome
Add gmt Park base class for Park based tools
Add ability for gmt Park::Base to run rex processes
Allpaths assemblies >3GB should run on 1TB machine
add conditions to CallR.pm.MutationSpectrum.R so that mutation-spectrum plots created in clin-seq will work with ggplot2 <= 0.8.9 and ggplot2 >= 0.9.X
remove unused method, execute_with_bsub

I am trying to improve a related method and discovered that this method
is not used.  I believe it is unused because `ack execute_with_bsub`
returned no matches and running an event model (ReferenceAlignment) did
not call the method.  Also, all tests pass with it removed.
InstData Import: hacky way to get read_lenth and set on instdata #FIXME!