Utility updates
Changed the behavior of append_stem to require less arguments.
It was annoying to have to put the delimiter as a separate argument.

fixed safe_makedir to not try to make a directory out of an
empty string or None.
Adapter read through trimmer added.

Uses cutadapt and some known adapter sequences to trim off reverse
complemented adapters from the end of reads with small insert sizes.
It also can trim off trailing polyA sequences as well.

Introduces a change to the YAML file. trim_reads: is no longer true/false
but can pass a parameter. To do the read through trimming, the
parameter is 'read_through'.

adapters are specified with adapters: [list_of_adapters]. A set of
known adapters is supplied; right now truseq and nextera are supported
as well as polya.

Non-supported adapters can be supplied as raw sequences under 'custom_trim'.
These extra sequences will not be reverse complemented though.