More documentation(added more scripts)
Updated documentation
Added version to all scripts and modules
Fixed bug dealing with empty lines in a runfile. Removed -d option from demultiplex
No longer tries to set UID on files. Misc other fixes. Readme updates
Formatter ignores config entries for platforms unless they are _in_ _out_ formatted
Misc fixes
Adding in two quick scripts to generate a graphic for qualities in a .qual file
Added ix_rename.py for renaming iontorrent read files. Better error output with abspath_or_error
Some more logging info as well as better checking to make sure midkey exists in a region
Initial addition of sanger_linker to link sanger read names from raw format to read format
sanger_linker now checks to see if the desitination exists. If it does then checks to see if the source directory matches the linksrc directory. If they do not exist it indicates that the sanger file is not uniquely named and generates an error message
sanger_linker.py now handles duplicate names much better. It uses runnum which should be a unique run number from the machine to name each link it generates which hopefully fixes the duplication problem. Made some additions and changes to the settings.cfg for the sanger platform to reflect this
Merged in new changes from dev
os.path.exists doesn't always work on symlinks
Ensure that ix_rename does not create broken links
Fixing up the documentation to match all the latest changes
More changes for documentation as well as getting errors reported in an easier to digest way
Documented dependencies
Small typo