numCPU parameter has no effect

[ptrebert]

Even with the bioconductor v1.0.0, it does not seem that the numCPU parameter (in the config) triggers multiprocessing (loaded in session: doParallel_1.0.15 and foreach_1.4.7).

I would expect that breakpointR reads the BAM files in parallel (1 CPU per BAM file), but they are read and processed sequentially.

[daewoooo]

The problem is numCPU is not properly read from the config file. numCPU works if set within the breakpointr() function. I will resolve this issue ASAP.