Initial commit.
Adding in more of the needed functions.
One bug fixed regarding the move from bin size in cache file names from e.g. "15000" to "15kbp".
Fixing binning to be [a, b) instead of (a, b], i.e. to contain the left end-point, but not the right.
Changed to .rds files for bin annotations, fixed one bug in the correctReadCounts().
Fixed one bug in correctReadCounts().
Merge remote branch 'origin/master'
Moved the download repo under account ccagc, fixed bugs in pooling script.
Merge remote branch 'origin/master'
Adding more functions, fixing some bugs.
Adding options to flag bins for filtering.
Fixed some typos.
Adding package Makefile, e.g. make install, make check, make Rd.
Minimal updates to dummy man/*.Rd files so that package passes R CMD check.
o Added Rdoc comments to *.R source files.
o Compiled Rdoc-to-Rd via 'make Rd'.  DON'T modify Rd files anymore.
Forgot to commit one Rd file.
o Added missing package dependencies to DESCRIPTION.
o Package passes R CMD check on R v3.0.1 with all OKs.
ROBUSTNESS: Added explicit argument names where possible.
ROBUSTNESS: Specifying integers as '1L' instead of '1'.
SPEEDUP: Replaced all rm(x) with rm(list="x"), cf. https://stat.ethz.ch/pipermail/r-devel/2013-May/066722.html
CLEANUP: Replaced an apply(x,2,sum) with rowSums(x).