Summary of changes in this version:
- Fix for #40 with reads not being found in cluster merging step. This was due to how different
Casava versions are handled. The original routine was correct but an issue lingered due to
this not always being invoked. - The above fixes an secondary issue that was causing the annotated repeat fraction to be reported
as being lower than in reality, though this has been resolved. - Add YES/NO boolean for setting in-memory analysis in configuration. This should be more intuitive
than the 1/0 form (which will still work). - Remove the 'each' hash loop syntax from all classes. This is known to cause some issues, especially
when adding/removing keys so we changed all methods to use 'keys' instead. - Label repeat summaries in log as either theoretical or biological if they are from just clustering or
clustering + annotated repeats, respectively.
See the "Changes" file for more information.