HyLiTE version 0.1.1:

1. Propagation via Parameters, a singleton class
2. Added an option allowing to pickle every n genes (default put to 50)
3. The pickling is now done on a .tmp file which is then renamed (so a crash during the pickling won't result in a data loss)
4. The results of the call to the binomial distribution are now stocked, resulting in significantly less call (from 60 000 to 260) for a negligible amount of time (ppf took more than half of HyLiTE running time prior to this modification)

Profiling HyLiTE over a small dataset (test5ter: 7M of reads) revealed:
 - ~3/4 of the time is now spent in Lane.update()
 - ~1/10 of the time is spent on phred_quality() (as we don't use quality for our calculus, we could just comment the line) (this function operate inside Lane.update())
 - ~1/10 is spent in lane.get_count()
 - ~2/10 is spent getting parameters values for a ridiculous number of calls (>20 millions! ... close to the number of base of all the reads together... )

Plans:
 - disable phred_count
 - weave Lane.update / Lane.get_count (mean that we gain dependency to a C compiler)
 - reduce the number of call to Parameters (stock the values rather than calling for them again)


git-svn-id: svn+ssh://svn.code.sf.net/p/hylite/code@38 e9d9261a-d21a-4311-8af8-dfff02415336