Added configuration file for processZips.sh so that it is more easly adapted to different environments
Restructured dependency folder to match what processZips.sh expects
Changed configuration code to not complain if it cannot find a program the first time
- Fixed configuration line to BWA mem so that shell variables expand
  correctly.
- Some small formatting issues
- Collapsed a pair of sed rules to a single equivlent rule
- Some minor logic restructuring of the program mainly to turn features
  off that are not used in all environments.
- Disabled bash debugging in the script
- Made the number of threads for GATK controlled by a variable
- Fixed typo where a the same paired end file was used for both ends
- Added some error handling for abyss outputs
Only using 1st column of RemoveFromAnalysis.txt
update
changing how zero coverage is handled in vcftofasta.sh
update
update
update
Merge branch 'master' of https://github.com/stuber/SNP_analysis

Conflicts:
	bin/processZips.sh