exposes --cov param

[zlskidmore]

removes hardcoding of --cov param to NULL and small bug fix where seg2gr complains that list is not supplied

[ShaiberAlon]

@zlskidmore , thank you for this pull request. Did you try this fix with your data? Did it work for you?

[zlskidmore]

not yet, I am digging further into it today. I am still getting a "index out of bounds error"

[zlskidmore]

@ShaiberAlon I did get this working, the remaining issues were calls to gr.sub that had to be commented out. I had modified the GC and MAP files to correspond to my bam files and subsequently my coverage files which all are chr1, chr2..... It looks like gr.sub is called on the gc and map files regardless of the coverage input (but is not called on the coverage input at all).

Happy to put in a pull request for this as well, but there are a couple of ways to go about it and I wasn't sure if there was a preference on how to handle this type of situation