Added rePreProcSample to NAMESPACE

Merge remote-tracking branch 'upstream/master'

New version (0.6.0). Removed emcncf2 and added udef option for genome…

… build.

Fixed a typo in inst/extcode/README.txt

Added a line to ChangeLog to indicate integer overflow bug fix.

Fixed NAMESPACE and facets-package.Rd to address messages in R CMD check

fix warning related to flat sample

added a flag for the new addition to findDiploidLogR

fixed DESCRIPTION to bump version number

fix bug for negative cn in emcncf