Updates for issue 90#105
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Change filtering criteria: DO NOT filter out pathogenic germline variants. TERT always to report. The genes with one of these 2 conditions will be reported with highest priority in PRONTO report. These "rescued" variants should have a separate column (at the far right of the table) to verify this. Separate column "Filter rescued", values are "Yes" or empty.
… should not appear in the tables appearing on the right of slides in report, but only printed this column in the summary table in slide 8.
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@marrip I just got further request for this issue. I updated in the issue 90. There will be some further new codes coming soon. |
ok, then I will wait with the review until you tell me to start |
… rescued variants which are not include in Filter0-3.(Last table in the report)
…to develop_issue90
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will start latest tomorrow 🙂 |
marrip
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marrip
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hey Xiaoli! I had a couple of questions and a suggestion. I am also working on a refactoring of some of the parts but need your input first
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Looking at the remaining changes it seems that a lot of the fixes are to handle different column numbers of the combined tables, replacing tabs with linebreaks or vice versa and making data unique. I would suggest we rework this and use pandas instead which would make reading, filtering, combining and writing to file a lot easier. What do you think? |
This is removed in main branch, not sure why it is existing here. Co-authored-by: Martin Rippin <74295098+marrip@users.noreply.github.com>
…to develop_issue90
…01-A08_small_variant_table_forQC.tsv Remove old file due to some format issues.
Correct format issues.
…-D01-P01-A08_MTB_report.pptx Remove old testing output.
Latest testing output report.
…01-A08_MTB_report.pptx to test_data/ous/test_files_for_PRONTO_newFunctions/output/IPD2225-D01-P01-A08_MTB_report.pptx output folder added
Refactor issue90
2 participants
Change filtering criteria:
The gene with one of these 2 conditions will be reported with highest priority in PRONTO report.
These "rescued" variants should have a separate column in tables to verify this. Separate column "Filter rescued", values are "Yes" or empty.