Merge pull request #14 from chapmanb/master

Merge from Brad upstream
Merge branch 'recursive_shell_expansion'
Fix bug when lane trimming is skipped.
Merge pull request #164 from porterjamesj/trim-fix

Fix bug when lane trimming is skipped, thanks to @porterjamesj.
Substitute qualimap QC run with bamtools stats. Provide a more lightweight approach until we can decrease qualimap run times
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Finalization of cn.mops implementation for CNV calling: create BED file with copy number reports and split results by batch samples
Fixes for cn.mops CNV calling: iterate over all chromosomes and collect results by sample
Generalize cn.mops to support tumor/normal paired CNV calling. Fix code issue preventing runs on non-autosomal chromosomes
Additional cn.mops fixes for tumor/normal case: ensure consistent windowlengths and calculate fractional counts
Update GRCh37 and hg19 genome resources with COSMIC VCFs
Added analyze unique starts by read depth.

Generates a plot of this metric, useful for flagging problem libraries.
Fixed bug with memoization of cutadapt trimmed files.
Add memory requirements for bowtie2 and tophat2.
Moved library complexity calculation to qc.

Returns a dictionary of the calculations and complexity estimation of
the library for use with the new qc file generator.
Added statsmodels to the list of conda packages to install.
Update whole genome benchmarking example to use NIST GiaB reference instead of our custom set of calls
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Remove standalone script. Add complexity metric to summary report.
Added reservoir sampling.