Fix bug in recognizing p.(=)

Release 2.0.10

Fix transcript mappings containing no exons

For transcripts without any UTR and CDS entries in the NCBI Mapview
file (seems to happen for  predicted genes), we generate one exon
spanning the entire transcript.

Fix typo in docs

Fix incorrect coloring of protein sequence positions

Use the Flask auto reloader in the debug server

Uncertain stop codon in protein descriptions (fs and ext)

When a variant results in a frame shift or extension and we don't
see a new stop codon in the RNA, the protein description should use
the notation for an uncertain stop codon, e.g., `p.(Gln730Profs*?)`
instead of `p.(Gln730Profs*96)` where 96 is just the last codon in
our transcript [1].

To detect this, we now use `to_stop=False` in our `.translate()`
calls, since that will explicitely return `*` characters for stop
codons.

We also slightly fix the coloring of changes in the protein sequence
where previously changed stop codon characters where not included.

[1] http://www.hgvs.org/mutnomen/FAQ.html#nostop

Dog assembly

Release 2.0.9

Usability improvements in reading DNA for description extractor

Don't trust encoding auto-detection when decoding

Use chardet instead of cchardet

Issue #50 showed a problem in our file encoding detection, caused
by our cut-off for the confidence as reported by the cchardet [1]
library:

    >>> import cchardet
    >>> s = u'NM_000052.4:c.2407\u20132A>G'
    >>> b = s.encode('WINDOWS-1252')
    >>> cchardet.detect(b)
    {'confidence': 0.5, 'encoding': u'WINDOWS-1252'}

We require a confidence stictly greater than 0.5 and default to
UTF8 otherwise.

If, however, we try the same thing using the chardet [2] library,
we get a higher confidence for the same string:

    >>> import chardet
    >>> chardet.detect(b)
    {'confidence': 0.73, 'encoding': 'windows-1252'}

So the two obvious ways to solve this are:

1. Lower the confidence threshold.
2. Use chardet instead of cchardet.

We implement the second solution here, since it also removes a C
library dependency and we are not worried by performance.

Of course the detected encoding remains a guess which can still
be wrong!

[1] https://github.com/PyYoshi/cChardet
[2] https://github.com/chardet/chardet

Fixes #50

Add NG example to name checker website form

Configurable maximum input length for description extractor

Adds a `EXTRACTOR_MAX_INPUT_LENGTH` configuration setting, defaulting
to 50 Kbp.