Add in percent identity and alignment length filters

[microbemarsh]

In this PR, we added the capability to filter alignments by:

• percent identity --min-pid
• minimum alignment length --min-aln-len
• maximum alignment length --max-aln-len

Due to increased 16S primers in the new ONT sequencing kit we dont plan to implement the input min/max read length yet.

[kdcurry]

Version 3.6.0
--Output-unclassified now outputs a third sequence file for the filtered (pid or alignment length) reads. Filtered read count is also tracked in output abundance file

Bug for python versions 3.11+ fixed by enforcing integer keys in the frequency (f) dictionary