Fixed complexity calculation when there are few reads in the BAM file.
Improved memory handling: explicitly add in memory for system usage and keep fractional memory estimates. Intended to better work with restricted memory setups like SLURM scheduler and VMs
Improve test running with wrapper script: uses pre-installed version of nose local to installer provided Python and handles re-writing existing system configurations to use smaller test-specific genome data.
Ensure BAM indexes are up to date with BAM file, re-creating if not. Fixes #181. Provide better error reporting for problem lines when running BamIndexStats. Fixes #180
Correctly detect regions versus target BED files for FreeBayes. Avoid leaking internal changes in subset_variant_regions used to cleanly subset by regions
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.