Closed aguang closed 5 years ago
:exclamation: No coverage uploaded for pull request base (
master@b72505d
). Click here to learn what that means. The diff coverage is70.34%
.
@@ Coverage Diff @@
## master #23 +/- ##
=========================================
Coverage ? 70.34%
=========================================
Files ? 10
Lines ? 499
Branches ? 0
=========================================
Hits ? 351
Misses ? 148
Partials ? 0
Impacted Files | Coverage Δ | |
---|---|---|
qcdb/db_create.py | 0% <0%> (ø) |
|
qcdb/db_load.py | 30.23% <30.23%> (ø) |
|
qcdb/connection.py | 64.28% <64.28%> (ø) |
|
qcdb/tables_create.py | 65.71% <65.71%> (ø) |
|
tests/test_connection.py | 73.91% <73.91%> (ø) |
|
qcdb/parsers/parse.py | 82.52% <82.52%> (ø) |
|
qcdb/parsers/picardtools_parse.py | 85.71% <85.71%> (ø) |
|
qcdb/parsers/qckitfastq_parse.py | 87.5% <87.5%> (ø) |
|
tests/test_db.py | 95.06% <95.06%> (ø) |
|
qcdb/parsers/fastqc_parse.py | 95.55% <95.55%> (ø) |
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to clarify, we provide 3 picardtools metrics currently: insertsize_metrics
, alignment_summary_metrics
, and summary_gcbias_metrics
This first version uses mysql and has parsers for the programs qckitfastq, fastqc, and picardTools (including only CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics, and CollectGcBiastMetrics from picardTools). It contains a reference table for field names for each metric and program, a sample metadata table with SRS and SRX ids as well as library type, and metrics for each unique sample.
It does not have other sample metadata that would be taken from SRA. That is being worked on in #14, which will also include a script to populate thosefields post-hoc. Other than that it should be feature complete, and we can start populating it.