Replace indexed based lookup with dictionary lookup

[scanon]

This is to address a performance issue that was seen when uploading large metagenomes. The FastaGFF uploader using an index call to get the contig_length. This winds up being slow when there are 10M plus contigs. Fortunately there was already a dict of the same information. I'm not sure why that wasn't used in the first place. Testing shows this gives linear performance even for very large metagenomes.

[codecov[bot]]

Codecov Report

Merging #199 (bee2c55) into master (0b0b4f2) will decrease coverage by 6.33%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #199      +/-   ##
==========================================
- Coverage   74.41%   68.08%   -6.34%     
==========================================
  Files          11       11              
  Lines        2877     2886       +9     
==========================================
- Hits         2141     1965     -176     
- Misses        736      921     +185     

Impacted Files	Coverage Δ
lib/GenomeFileUtil/core/FastaGFFToGenome.py	88.54% <100.00%> (-0.80%)	:arrow_down:
lib/GenomeFileUtil/core/GenomeToGFF.py	29.69% <0.00%> (-46.67%)	:arrow_down:
lib/GenomeFileUtil/GenomeFileUtilImpl.py	49.47% <0.00%> (-23.35%)	:arrow_down:
lib/GenomeFileUtil/core/GenomeToGenbank.py	89.44% <0.00%> (-6.12%)	:arrow_down:
lib/GenomeFileUtil/core/GenbankToGenome.py	89.19% <0.00%> (-4.29%)	:arrow_down:
lib/GenomeFileUtil/core/GenomeInterface.py	79.44% <0.00%> (-0.35%)	:arrow_down:

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[Tianhao-Gu]

👍 LGTM