feat: seqvars effects filter #1833
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deps-report 🔍Commit scanned: 44fd935 Vulnerable dependencies4 dependencies have vulnerabilities 😱
Outdated dependencies42 outdated dependencies found (including 16 outdated major versions)😢
|
Gregoor
commented
Jul 23, 2024
Comment on lines
36
to
72
| // feature_truncation: 'feature truncation', | ||
| // frameshift_elongation: 'frameshift elongation', | ||
| frameshift_variant: 'frameshift variant', | ||
| // inframe_deletion: 'inframe deletion', | ||
| // inframe_insertion: 'inframe insertion', | ||
| // internal_elongation: 'internal elongation', | ||
| missense_variant: 'missense', | ||
| // mnv: 'MNV', | ||
| start_lost: 'start lost', | ||
| stop_gained: 'stop gained', | ||
| stop_retained_variant: 'stop retained', | ||
| stop_lost: 'stop lost', | ||
| // tandem_duplication: 'tandem duplication', | ||
| }, | ||
| 'Off-Exome': { | ||
| downstream_gene_variant: 'downstream', | ||
| intron_variant: 'intronic (coding transcript)', | ||
| // intergenic: 'intergenic', | ||
| upstream_gene_variant: 'upstream', | ||
| // exon_loss: 'exon loss', | ||
| }, | ||
| 'Non-coding': { | ||
| '3_prime_UTR_variant-exon_variant': "3' UTR exonic", | ||
| '3_prime_UTR_variant-intron_variant': "3' UTR intronic", | ||
| '5_prime_UTR_variant-exon_variant': "5' UTR exonic", | ||
| '5_prime_UTR_variant-intron_variant': "5' UTR intronic", | ||
| non_coding_transcript_exon_variant: 'non-coding exonic', | ||
| non_coding_transcript_intron_variant: 'non-coding intronic', | ||
| }, | ||
| Splicing: { | ||
| splice_acceptor_variant: 'splice acceptor', | ||
| splice_donor_variant: 'splice donor', | ||
| splice_region_variant: 'splice region', | ||
| }, | ||
| Structural: { | ||
| // structural: 'structural ', | ||
| // transcript_ablation: 'transcript ablation', |
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@holtgrewe all the commented out entries are present in the design, but missing in the API.
Most of them seem to be present here:
varfish-server/backend/seqvars/models.py
Lines 109 to 208 in 8d39e44
Should I leave them out for now, or uncomment them on the backend side (+migrations etc.)?
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Please leave as is, this is (sadly) still work in progress.
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(wip on the server side / backend) - will fix and adjust later, possibly after our common project
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #1833 +/- ##
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Coverage 91% 91%
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Files 653 653
Lines 36624 36624
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Hits 33567 33567
Misses 3057 3057 |
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