Fix paired bam detection in qc.
Merge pull request #235 from porterjamesj/patch-1

Fix paired bam detection in qc.

Thanks @porterjamesj!
Fix improper cufflinks directory file creation.

Thanks to @porterjamesj.

Closes part of https://github.com/chapmanb/bcbio-nextgen/issues/234.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen