Clean up alignments and mutations code

[stuckinaboot]

Notice: if you make significant changes to alignment or mutation identification code, the expectation is that the alignment output/mutation output with your changes will be equivalent to the alignment output/mutation output prior to your changes. Both alignment algorithms and mutation identification algorithms from the current code (as of 12/17/2020) have been validated extensively and the safest path forward for the time being is ensuring that code changes still output the same data. TODO @stuckinaboot : update this issue with a link to markdown on how to easily let others validate alignments/mutations

There are a number of code quality issues in the alignments and mutations files. The code efficiency and accuracy is fine and validated in our paper (if you have improvements feel free to suggest) but the code quality can be improved in the following areas:

• Remove commented code
• Remove unnecessary comments (e.g. old comments that say "Ask Mike", as I already checked with Mike, Dr. Schatz, years ago but hadn't removed the comment)
• Clean up code structure (e.g. break up dense functions into smaller/helper functions, using brackets with all if/else statements, etc.)

If you have any ideas for cleaning up the code in terms of quality, structure, documentation, etc. beyond these, they will be greatly appreciated.

Feel free to work on a single header or implementation file (.h or .m), or both the header and implementation file (.h or .m) within a section:

Relevant Mutation Files

1 Mutation Filter

• https://github.com/stuckinaboot/iGenomics/blob/master/iGenomics/BWT/BWT_MutationFilter/BWT_MutationFilter.h
• https://github.com/stuckinaboot/iGenomics/blob/master/iGenomics/BWT/BWT_MutationFilter/BWT_MutationFilter.m

Relevant Alignment Files

1 BWT Matcher Superclass

• https://github.com/stuckinaboot/iGenomics/blob/master/BWT_MatcherSC.h
• https://github.com/stuckinaboot/iGenomics/blob/master/BWT_MatcherSC.m

2 Core BWT Matcher (core alignment logic)

• https://github.com/stuckinaboot/iGenomics/blob/master/iGenomics/BWT/BWT_Matcher/BWT_Matcher.h
• https://github.com/stuckinaboot/iGenomics/blob/master/iGenomics/BWT/BWT_Matcher/BWT_Matcher.m

3 Aligning with insertions/deletions (uses edit distance)

• https://github.com/stuckinaboot/iGenomics/blob/master/BWT_Matcher_InsertionDeletion.h
• https://github.com/stuckinaboot/iGenomics/blob/master/BWT_Matcher_InsertionDeletion.m

Note: File names will stay the same but relative file path in the GitHub repo may change as #15 is addressed