Various bug fixes.
Merge tool:
- first merge unmapped reads
- added merge of remaining reads in the spread reads file
- fixed bug where merge loop skips reads at bounds
Compare tool:
- added check on rnext for batching reads to compare
- general clean up of the code
- removed parallel batching
User inteface:
- fixed typo causing the add-refid filter not to be added when just using elPrep for sorting
Added documentation strings.