Convert the tabs in the file to spaces, add more var_types to check
Fix the CMAP definition for SVDetect, the wrong column was defined in the makefile, causing SVDetect reading the wrong index for the chromosome
Fix SVDetect2vcf script, referenced non-existing keys from dictionary.
Make less dependent on the system distributed version of Python, now you can specify the python bin to use (e.g. from virtualenv with additional libs installed)
Rename makefiles, preparing for generic calling/starting the sub-pipelines
Add copyright information to all files
Several python fixes in syntax and visual processing
Let pindel also use the THREAD option, not it's own specific setting
Update the Delly wrapper for new version of delly
make -n fix
Merge branch 'master' of https://github.com/ALLBio/allbiotc2
Fix main makefile
Commit of working files 22-januri 2014
Changes to makefile definition to reduce the chance of recursive execution
Path config update
Proper merge
Always run prism run after breakdancer, redefined the ordering of execution (note this is not qmake compatible)
Refinements in each module makefile, optimisation in runtime for indel calling
Merge from master branch
clean repo, add author information