Nicking Hancock

This release incorporates changes to make bowtie2 alignment in CRISPRessoPooled more permissive (44dc9e7), and remove duplicate rows in the Alleles_frequency_table.txt due to reads being in the forward or reverse direction (0e08cd0).

When given a genome file, CRISPRessoPooled aligns reads to the genome using the Bowtie2 aligner. The legacy parameters were somewhat strict. The new parameters reflect the 'default_min_aln_score' parameter in allowing for substantially more indels and mismatches than previous.
The parameter --use_legacy_bowtie2_options_string has been added to use the legacy settings. Otherwise, the bowtie2 alignment settings will be calculated as follows:
--end-to-end - no clipping, match bonus -ma is set to 0
-N 0 number of mismatches allowed in seed alignment
--np 0 where read (or ref have ambiguous character (N)) penalty is 0
--mp 3,2 mismatch penalty - set max mismatch to -3 to coincide with the gap extension penalty (2 is the default min mismatch penalty)
--score-min L,-5,-3*(1-H) For a given homology score, we allow up to (1-H) mismatches (-3) or gap extensions (-3) and one gap open (-5). This score translates to -5 + -3(1-H)L where L is the sequence length