Gel-coverage

----------------------------

* Minor changes
- Implemented a truncated binary backoff retry policy for CellBase and PanelApp connections.
- Fixed a bug with some percentages truncated to only 1 decimal place.
- Logs are now more controlled when missing regions are found. Also, log level is configurable when using the module as a Python library, default log level is INFO.
- PEP8 fixes

----------------------------

* Minor changes
- Upgrading required numpy version to 1.10.4

----------------------------

* Major changes:
- Coverage standard deviation is added to set of coverage metrics
- Coverage statistics aggregated for autosomes
- Some fields are renamed and every field name is not stored as a constant in the code, so renaming is not so painful.

* Minor Changes:
- Fixed bug when all transcripts in a panel have been filtered out
- Longs list of genes (>99) are never printed to logs

----------------------------

* Minor Changes:
- Using setuptools find_package() to create a proper python package

----------------------------

* Minor Changes:
- Fixed bug when iterating whole genome in chunks
- Fixed bug when trying to create an unexisting BED file for whole genome analysis
- Add flag to avoid running analysis on the coding region
- Added execution times to documentation
- Ported shell script for biohpc

----------------------------

* Major Changes:
- Output in machine readable format, JSON.
- All required (so far) coverage statistics merged in the same module.
- Reading panels from PanelApp webservices.
- Reference from CellBase is now read using the Python client, pycellbase.
- Added percentages of bases over certain coverage thresholds and a measure of uneveness at chromosome and whole genome levels.