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QC Database
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fix(fastqcParse): fastqcParser now accounts for missing modules #29

Closed aguang closed 4 years ago

aguang commented 4 years ago

fastqcParser used to assume you would have data for all 11 modules, however this is not the case for some samples as they may be missing tile quality because they are not Illumina data, or they may not have overrepresented sequences. In that case the indexing for modules became erroneous, which triggered issues with column names and data insertion. It is now fixed so that it only parses for modules which it finds in the fastqc_data.txt file.

close #28

codecov[bot] commented 4 years ago

Codecov Report

Merging #29 into master will increase coverage by 0.24%. The diff coverage is 94.48%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #29      +/-   ##
==========================================
+ Coverage   88.79%   89.04%   +0.24%     
==========================================
  Files          11       13       +2     
  Lines         607      657      +50     
==========================================
+ Hits          539      585      +46     
- Misses         68       72       +4
Impacted Files Coverage Δ
tests/test_db.py 96% <100%> (-1.23%) :arrow_down:
tests/test_parse.py 100% <100%> (ø)
qcdb/db_load.py 70.73% <66.66%> (+1.21%) :arrow_up:
qcdb/parsers/fastqc_parse.py 91.46% <88.37%> (-4.1%) :arrow_down:
tests/conftest.py 95.34% <95.34%> (ø)

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