Update CITATION.
Rsamtools has renamed parameter isNotPrimaryRead to isSecondaryAlignment, update binReadCounts() accordingly.
Merge branch 'master' into devel

Conflicts:
	R/binReadCounts.R
	man/binReadCounts.Rd
Add a note for error messages originating from CGHcall.
Fix applyFilters() to ignore the residual filter for those chromosomes for which it does not exist (X and Y).
Update NEWS.
Bump development version number to 1.3.3.