Disambiguate and fusion fields updated in docs

Hi Brad,
I've included some documentation on fusion detection and disambiguation.
Whenever you think this is good to be included, please merge
qsignature implementation

fix merge

add qsignature to multitask

add qsignature to qcsummary

remove slice from bam.__init__

remove weird space
add total samples, and similar sample to report
Ensure we install data on upgrade if genomes, aligners or toolplus specified #537
Merge pull request #533 from mjafin/patch-3

Disambiguate and fusion fields updated in docs
add history changes, and run only if qsign is installed

fix variable name
Trimming overhaul, removal of decompression of FASTQ files.

1) Don't uncompress FASTQ files while trimming.
AlienTrimmer does not work on gzipped files, and the recent skewer paper shows
AlienTrimmer is not as sensitive as the other trimmers, so it is time to
retire it.

http://www.biomedcentral.com/1471-2105/15/182

2) cutadapt + skewer to trim
cutadapt has had the weakness of being slow and not handling paired data
particuarlly well. We run cutadapt without removing any reads and then use
scythe to remove the reads that are too short, streaming between the two so we
don't touch disk.  With the 1.4 release of cutadapt, trimming has been sped up
a ton, especially with gzipped files so this should be fast.
Merge pull request #538 from mjafin/master

RNA-seq variant calling preparations
Merge qsignature datadict changes
Merge branch 'lpantano-upstream'