Support gRNA1 error tolerance

[marissafujimoto]

Description

Previously the pgmap algorithm had taken only perfect gRNA1 matches. This change adds support for gRNA1 error tolerance of up to 2 substitutions. The algorithm involved precalculates and caches every mutated gRNA in the library. As such it's memory and time complexity is O(c * n^k) where c is the number of unique gRNAs, n is the length of the gRNAs and k is the number of errors tolerated. With error tolerance of 2 this uses around 20 seconds to precalculate the cache and <5 gb of memory. Error tolerances over 2 result in error, but in principle could be supported on machines with enough memory.

Type of change

• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

How Has This Been Tested?

Added unit tests. Run with pip install . && python3 -m tests

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules