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compbiocore / qcdb

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Issue 8 #15

Closed JRWallace closed 5 years ago

codecov[bot] commented 5 years ago

Codecov Report

Merging #15 into devel will increase coverage by 12.25%. The diff coverage is 81.08%.

Impacted file tree graph

@@            Coverage Diff             @@
##            devel     #15       +/-   ##
==========================================
+ Coverage   55.34%   67.6%   +12.25%     
==========================================
  Files          10      10               
  Lines         421     392       -29     
==========================================
+ Hits          233     265       +32     
+ Misses        188     127       -61
Impacted Files Coverage Δ
qcdb/parsers/picardtools_parse.py 100% <100%> (+100%) :arrow_up:
tests/test_parse.py 100% <100%> (ø) :arrow_up:
qcdb/db_load.py 27.58% <12.5%> (-4.13%) :arrow_down:

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aguang commented 5 years ago

Looks good, but JSON is inserted with field names in quotes, leading to JSON strings like:

"{\"ACCUMULATION_LEVEL\": \"All Reads\", \"READS_USED\": \"ALL\", \"WINDOW_SIZE\": \"100\", \"TOTAL_CLUSTERS\": \"57196247\", \"ALIGNED_READS\": \"111280178\", \"AT_DROPOUT\": \"6.174107\", \"GC_DROPOUT\": \"0.000078\", \"GC_NC_0_19\": \"0.539031\", \"GC_NC_20_39\": \"1.043416\", \"GC_NC_40_59\": \"0.966219\", \"GC_NC_60_79\": \"1.178836\", \"GC_NC_80_100\": \"1.449855\", \"SAMPLE\": \"\", \"LIBRARY\": \"\", \"READ_GROUP\": \"\"}"

This will be a problem since they are non-alpha character field names. The field names should have their \" stripped.