feat: Add bgzip index support for fsspec objects

[ggydush]

Currently, for remote files (fsspec objects), there is support for pre-computed .fai files, but no support for pre-computed .gzi files. This means that the entire file must be read to re-compute the .fai file as well as the .gzi file (looks like this re-computation of the index was added recently #164)

I have implemented the .gzi support in a similar fashion to the .fai support. All of the tests pass, and I created all combinations of local/remote with the following code:

import s3fs
from itertools import product
from fsspec.core import OpenFile

import pyfaidx


fs = s3fs.S3FileSystem()
files_local_and_remote = [
    (
        "/local/ercc.fa.gz",
        "s3://.../ercc.fa.gz",
    ),
    (
        "/local/ercc.fa.gz.fai",
        "s3://.../ercc.fa.gz.fai",
    ),
    (
        "/local/ercc.fa.gz.gzi",
        "s3://.../ercc.fa.gz.gzi",
    ),
]
combos = list(product([0, 1], repeat=3))
fs = s3fs.S3FileSystem()
for combo in combos:
    files = []
    for file_index, file_options in zip(combo, files_local_and_remote):
        fname = file_options[file_index]
        if fname.startswith("s3://"):
            fname = OpenFile(fs, fname, mode="rb")  # type: ignore
        files.append(fname)
    fa = pyfaidx.Fasta(files[0], indexname=files[1], gzi_indexname=files[2])
    print("is_remote: ", combo, files, len(fa.records))

[codecov]

Codecov Report

❌ Patch coverage is 68.75000% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.63%. Comparing base (de5cdf8) to head (f8f960c).
⚠️ Report is 2 commits behind head on master.

Files with missing lines	Patch %	Lines
pyfaidx/__init__.py	68.75%	10 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #232      +/-   ##
==========================================
- Coverage   78.96%   78.63%   -0.34%     
==========================================
  Files           2        2              
  Lines        1160     1184      +24     
==========================================
+ Hits          916      931      +15     
- Misses        244      253       +9     

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[mdshw5]

Hey @ggydush this looks great, and is actually something I meant to do in v0.9.0! Thanks for providing the test code for this. I'm going to release a quick bug fix version with your changes.