Crispresso

> Fixed alleles plot when common alleles contain 'N'

> Added --max_paired_end_reads_overlap for FLASH merging step

> CRISPRessoPooled looks for cleaned/slugified names (produced by CRISPResso) for combining pools.
> Fixed a Warning: invalid value encountered in double_scalars y_label_values=np.arange(0,y_max,y_max/6.0)
> Fixed a problem with Pandas ILovePandas where if a subset returns a single
row, it returns a scalar instead of a DataFrame. This resulted in an
error: ERROR: ("'numpy.int64' object is not iterable", u'occurred at index 0')

> Fixed bug in CRISPResso when writing the Quantification_of_editing_frequency.txt file. 'nan's in the np.sum cause the writing to fail, resulting in no output.

> Implemented parameter 'bowtie2_options_string' in CRISPRessoPooled for changing parameters passed to bowtie2
> Added debug functionality to print most common unaligned reads in cases
where less than half of reads align in CRISPRessoPooled

> Fixed the cup!
> Fixed allels around cut site plot with seaborn >= 0.8.0
> Added the option --allow-outies to flash to also try combining read pairs in the "outie" orientation