TODO

* Add robust estimate for mean and std (Done);
* Flexible input for findHotspots (Done);
* Allow chromosome name to have more relaxed format (DONE);
* Multiple core support (quick and dirty fix of PP);
* Control short read redundancy internally;
* Support BAM input;
* Check number of replicates for different testing methods (DONE)
* Delete files using PERL API instead of 'rm' (done for main program)
* findHotspots.pl column meaning Wiki (DONE)
* Remove intermediate files even if the program exits (DONE)
* Re-organize modules and documentation (DONE)


====These are the modules included in diffReps:====
MyBioinfo::Common
MyBioinfo::Math
MyBioinfo::NBTest
MyShortRead::ChromBed
MyShortRead::MyShortRead
MyShortRead::SRBed
PJ::Database::Root
PJ::Genome
diffReps::ChromaModSite
diffReps::DiffRes


====Some future improvements to think about:====
* PCR redundancy removal and its impact on differential analysis
* Better negative binomial test algorithm
* MapReduce implementation
* Better normalization algorithm
* Re-implementation in Python
* Down-stream annotation and analysis