upgrades bismark to 0.10
no longer sorts bam by defaults (methylation extractor can't take that)
methylation extractor can now handle bam files directly
bismark takes an argument -p, which it passed
directly to bowtie2 for *each* bowtie2 process
it runs.

This is bad on a shared cluster since it uses
double the cpus compared to the number of slots requested.

This changes the meaning of -p from 
"number of threads used by each bowtie2 process"
to 
"number of total threads used by bismark"

(if a --non_directional flag is ever added, we'll need to divide by 4 instead of 2)
bam_path is just a plain variable, not a member of args
Merge pull request #42 from bwlang/bismark_0.10

upgrades bismark to 0.10