Fixing minor things found when preparing for validation testing

[johandahlberg]

I've been fixing a few small things, in preparation for validation testing.

A lot of it cosmetic, improving documentation and output messages. However, I also found and fixed a but which would call read 2, read 3. Since there are a few different things going on here it might be easiest to review this PR commit by commit, instead of looking at the full diff.

[codecov[bot]]

Codecov Report

Merging #26 into master will decrease coverage by 0.09%. The diff coverage is 100%.

@@            Coverage Diff            @@
##           master      #26     +/-   ##
=========================================
- Coverage   93.54%   93.44%   -0.1%     
=========================================
  Files          16       16             
  Lines         480      488      +8     
=========================================
+ Hits          449      456      +7     
- Misses         31       32      +1

Impacted Files	Coverage Δ
...heckQC/handlers/undetermined_percentage_handler.py	95.83% <ø> (ø)	:arrow_up:
checkQC/run_type_recognizer.py	94.04% <100%> (ø)	:arrow_up:
checkQC/handlers/q30_handler.py	95.45% <100%> (ø)	:arrow_up:
checkQC/__init__.py	100% <100%> (ø)	:arrow_up:
checkQC/handlers/cluster_pf_handler.py	95.45% <100%> (ø)	:arrow_up:
checkQC/parsers/interop_parser.py	97.14% <100%> (+0.71%)	:arrow_up:
checkQC/handlers/reads_per_sample_handler.py	96.15% <100%> (+0.15%)	:arrow_up:
checkQC/config.py	92% <0%> (-2%)	:arrow_down:

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