Cnvkit

- Aesthetic improvements to plots
- Fixed an edge case where a very small BAM file could mistakenly appear to be
unsorted.

- Enable `batch` to be run without specifying tumor samples, in order to only
create a reference.
- Copy ratios are now re-centered at the smoothed "mode" (peak density) rather
than median, for better behavior on samples with many large-scale losses.
- Minor fixes and improvements to several safety checks in response to feedback
from users.

This is a bugfix release.
- `coverage`: Allow spaces in gene names.
- `target`: If gene names are not provided (BED3 format), use a default gene name "-". (Previously, the generated targets BED file would cause `coverage` to crash later.)
- Fixed the math underlying the edge/density correction.

- `antitarget`: Choose an appropriate default minimum bin size based on the user-provided average bin size.
- `breaks`: Added an option `--min-probes`, which applies to both sides of the detected breakpoint within a gene.
- `export`: Fixed the `nexus-basic` format to work with Biodiscovery Nexus Copy Number again.
- `target`, `refFlat2bed.py`: Handle overlapping gene annotations a little better.
- Made the dependency on SciPy "soft", only triggered when using the segmentation algorithm `haar`.

Updated dependency versions of Python packages numpy and matplotlib to match Ubuntu 12.04 package versions. This fixes a confusing installation issue related to having an old version of Biopython already installed.