updated cleancigr to actually work. refactored into its own method and added unit test
removed comment from bamutils count header - makes it difficult to import into R.
don't try to iterate on a string
modifications to better deal with tags
rewrote properpairs to sort the inputs on disk and read pairs that way... it might be faster
added support for user-defined tmpdir
usage doc update
tmp files are now compressed
doc update
added TODO
Merge branch 'working' of ssh://github.com/ngsutils/ngsutils into working