Is it possible to provide a switch for verbosity in ChIPQC that is passed on to the use of shiftApply? Or for shiftApply's output to respond to suppressMessages?
If I use ChIPQC inside an Rmd document, I get many lines like this in the output:
Calculating shift for chr1
1/300 2/300 [...] 299/300 300/300
I think I've tracked this down to a call to shiftApply with verbose=TRUE.
This output is not suppressed when wrapping ChIPQC in suppressMessages(). It's fine when running interactively, i.e. it doesn't print a new line for each iteration, but when run inside an Rmd it produces many lines of output which are annoying to scroll through. It'd be great to be able to suppress this with suppressMessages(), or turn it off with a verbosity switch. It seems like shiftApply uses cat() to print the message, I'm not sure if it's possible to keep the same behaviour when running interactively (i.e. updating the iteration number on the same line) if using message() instead.
I'm not sure whether this is better dealt with at the S4Vectors or ChIPQC level.
