non-UCSC chromosome nomenclature & gzipped counts

[WardDeb]

Hi,

First of all thanks for the software !
I've encountered two 'issues' when running this for my data:

• when using an 'ensembl' based genome (forged BSgenome myself), the chromosomes are named 1,2,.... The pattern matching under list.files thus fails (i.e. 1.rda, 11.rda). I've changed this just a file.path, as I think it's fair to assume that (even in the UCSC case) there'll always be one (and only one) file matching.
• the write.table - gzip chain for writing out the counts failed on our system (relatively slow disks), the workaround for this is to directly write out the counts file.

Cheers,

WardDeb

[mireia-bioinfo]

Hi!

Thank you so much for taking the time to fix this 'issues'. I've now merged them into the master branch. 😄