Fixed complexity calculation when there are few reads in the BAM file.
Fix for trimming single-end lanes.
Fixed complexity calculation when there are few reads in the BAM file.
Brought changelog up to date.
Added sorting via sambamba.
On whole-file complexity plotting, shuffle the start sites first.
Ensure files are name-sorted before disambiguation.
Add sorting via sambamba.

Note: this uses the header in the BAM file to figure out if it is
sorted already.
Fix for trimming single-end reads.
Add ability to subsample during the complexity calculation.
Added integration test for explant analysis.
Removed disambiguation step from stock RNA-seq integration test.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Merged fixes.
Fix to the explant unit test.
Updated history with sorting changes.