add docs for qsignature and kraken, and remove E321(PEP8) from qsignatur...

sorry to do another pull request. Just wanted to fix my very bad practices for python coding style, and add some documentation. :/

thanks Brad for your patient!
thanks Rory, you saved me

On 08/07/2014 03:42 PM, Rory Kirchner wrote:
>
> In bcbio/pipeline/qcsummary.py:
>
> > @@ -107,7 +110,7 @@ def _run_qc_tools(bam_file, data):
> >          cur_metrics = qc_fn(bam_file, data, cur_qc_dir)
> >          metrics.update(cur_metrics)
> >      ratio = bam.get_aligned_reads(bam_file, data)
> > -    if ratio < 0.60 and data['config']["algorithm"].get("kraken", False) and data["analysis"].lower() == "rna-seq":
> > +    if ratio < 0.60 and data['config']["algorithm"].get("kraken", False) and data["analysis"].startswith("rna-seq"):
>
> I think that .lower() needs to be in there, otherwise capitalization 
> issues in the input YAML file will make that fail. We should just 
> lowercase it when we read in the config file though.
>
> —
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> <https://github.com/chapmanb/bcbio-nextgen/pull/543/files#r15958715>.
>