Feature/ganon core io

[pirovc]

Change ganon on c++ side to work with minimal input. Now, the LCA file is not written by default and the report file (rep) is the default output.

ganon-build

default input:

• fasta file(s)

optional input:

• seqid start end binid (if not provided build ibf with one file per bin)

output:

• ibf

ganon-classify

default input:

• ibf
• fastq file(s)

optional input:

• map (target binid)
• tax (node/target parent [rank] [name])

default output:

• rep (no map ->output binid as target. no tax -> no lca)

optional output:

• lca
• all
• unc

[codecov-commenter]

Codecov Report

Merging #177 (291432d) into dev (9921af1) will increase coverage by 0.04%. The diff coverage is 84.41%.

@@            Coverage Diff             @@
##              dev     #177      +/-   ##
==========================================
+ Coverage   77.98%   78.02%   +0.04%     
==========================================
  Files          22       22              
  Lines        2516     2585      +69     
==========================================
+ Hits         1962     2017      +55     
- Misses        554      568      +14     

Impacted Files	Coverage Δ
src/ganon/classify.py	88.23% <ø> (ø)
src/ganon-build/include/ganon-build/Config.hpp	43.28% <37.50%> (-0.27%)	:arrow_down:
...c/ganon-classify/include/ganon-classify/Config.hpp	50.56% <56.25%> (+0.24%)	:arrow_up:
src/ganon-classify/GanonClassify.cpp	84.03% <89.60%> (+0.43%)	:arrow_up:
src/ganon-build/GanonBuild.cpp	74.72% <91.81%> (+3.75%)	:arrow_up:
src/ganon-build/CommandLineParser.cpp	87.87% <100.00%> (ø)
src/ganon-classify/CommandLineParser.cpp	84.52% <100.00%> (+0.57%)	:arrow_up:
src/ganon/config.py	77.77% <100.00%> (+0.07%)	:arrow_up:

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