Feature/parse large files low memory

[willgdjones]

This PR implements functionality to efficiently parse large VCF files without needing to decompress them. It also provides functionality to specify a set of rsids to extract from the file:

df = SNPs(bytes_data, rsids=["rs1", "rs2"]

This functionality only works when feeding in a bytes_data object, which needs to be a valid, gzip compressed byte-string.

I am able to extract rsids from an output of an imputation pipeline which is a VCF file ~450mb compressed in ~ 1 minute.

This should be merged after #32.

[willgdjones]

I think I need to match my black settings with yours. What editor settings do you use?

[apriha]

I think I need to match my black settings with yours. What editor settings do you use?

Just the default settings, integrated with PyCharm as an external tool: https://github.com/psf/black#editor-integration . You can run black --check --diff . before a commit to see if it would reformat any files.

[codecov-io]

Codecov Report

Merging #33 into develop will increase coverage by 1.4%.
The diff coverage is 96.42%.

@@            Coverage Diff             @@
##           develop      #33     +/-   ##
==========================================
+ Coverage    89.15%   90.56%   +1.4%     
==========================================
  Files            5        5             
  Lines         1097     1123     +26     
  Branches       196      204      +8     
==========================================
+ Hits           978     1017     +39     
+ Misses          73       60     -13     
  Partials        46       46

Impacted Files	Coverage Δ
src/snps/__init__.py	94.11% <100%> (+0.07%)	⬆️
src/snps/io.py	87.32% <95.74%> (+1.69%)	⬆️
src/snps/resources.py	94.33% <0%> (+3.77%)	⬆️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update a876341...f891388. Read the comment docs.

[willgdjones]

Ok! I've matched the settings now.

[willgdjones]

Hi @apriha - the refactoring that you've made to this PR looks good to me, thanks for doing so.

[apriha]

Thanks again @willgdjones ! Let me know if you agree with the latest commits and I'll merge the PR.

[willgdjones]

Those changes look good @apriha !