Single threaded optimization

[marissafujimoto]

Description

Addresses some of #13. I ran pgmap under a profiler (vizviewer) and saw that the hamming function and the file parsing was taking the most time. We have been using seq.io for fastx parsing and it is not optimized for our use case (insofar as it parses then discards a lot of information about quality, coordinates, etc). I switched to just using python built-ins to parse fastx and that was ~2x improvement on my machine. Then using the levenshtein package for the sequence alignment functions which added a small boost as well.

To give a rough idea of performance we are looking at < 15 minutes to run on ~10gb fastq files on my macbook air m3. Then on the hutch cluster it may be 5x that so a bit over an hour for a typical file.

Dependent on #14

Type of change

Optimization. No functional change.

How Has This Been Tested?

Tests coverage unchanged.

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

[cansavvy]

This looks great and sounds like its a great start to making the code quicker!

[cansavvy]

I'm going to go ahead and merge unless you have any issues @marissafujimoto !