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chore: refactor DB create #456

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chore: refactor DB create #456

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tedil
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@tedil tedil commented Jun 10, 2024

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tedil and others added 30 commits April 30, 2024 14:58
@tedil
setup pprof, criterion, flamegraph, dhat and coz
52343b9
@tedil
add criterion benchmark for consequence prediction (seqvars)
e516fd3
@tedil
add hgvs bench
9db7cd5
@tedil
enable flamegraph for hgvs bench
8e82a06
@tedil
rename bench function
14f6d14
@tedil
update noodles (but not yet vcf), use local versions of hgvs-rs and a…
27c3e27 
…nnonars for profiling
@tedil
use packaged annonars
fc75833
@tedil
add perf profile
5ac7d0a
@tedil
.
3c1c6ea
@tedil
extract actual record annotation method from run_with_writer
98c986a
@tedil
some clippy lints
a7fc362
@tedil
enable both async vcf reading and writing by default
71283fa
@tedil
… don't forget to flush
0aa9f5b
@tedil
pin specific hgvs-rs and seqrepo versions
ee70689
@tedil
remove annotation bench
6c2e81a
@tedil
actually disable all criterion benches for now
9c2b24c
@tedil
switch to noodles group
68df551
@tedil
more adaptations to use noodles group
503ffa2
@tedil
cherry picked noodles updates from dependabot branch
84b29ac
@tedil
merged
a2a4325
@tedil
more noodles adaptations, ditch bcf for now
dbce3fa
@tedil
remove benches
cf4279d
@tedil
clippy lints
230c423
@tedil
mark test_with_maelstrom_reader as async fn
1d7cd3c
@tedil
fix strucvar ids
1583ce0
@tedil
adapt to noodles new Genotype type
39bc5d1
@tedil
bump MSRV
384f37d
@tedil
flatten
db59485
@tedil
remove duplicated bounds on P
759c17f
@tedil
actually use constructed genotypes
de03415
tedil added 30 commits June 28, 2024 12:53
@tedil
report partial transcripts; adapt to mane-txs/tag-tsv column changes
1ae711c
@tedil
way more cleanup (wip)
ae0b411
@tedil
discard those entries for a reason, not for no reason:D
190c273
@tedil
way more cleanup, part 2 (wip)
bfd3241
@tedil
way more cleanup, part 3 (wip)
cb27124
@tedil
way more cleanup, part 4 (wip)
380e03b
@tedil
way more cleanup, part 5 (wip)
75dcdc8
@tedil
way more cleanup, part 6 (wip)
e38ee3d
@tedil
way more cleanup, part 7 (wip)
cb73bfd
@tedil
don't forget to provide the accession to filter on...
8e2ff2f
@tedil
don't list grafted transcripts as discarded
5a1b62d
@tedil
filter missing gene symbols early
8422adf
@tedil
reorder instructions for less cloning
619bf03
@tedil
mark discards for children/parent relations
61fae81
@tedil
fixed sort order in txdb
b95941f
@tedil
update insta snapshots to match output order
4a7d7b2
@tedil
update insta snapshots to match output order, test label file columns…
25f36ac 
… adapted
@tedil
test output ordering
3412766
@tedil
clippy lints, some comments
7f59789
@tedil
more clippy lints
23d3336
@tedil
move rss traces into main run
bb6166a
@tedil
also retrieve tags for genes and hgnc ids
4a7d591
@tedil
allow clippy lints for explicitness at that point
925a78e
@tedil
dedup tags for display
ba1085a
@tedil
fix merge logic
b5aa022
@tedil
fix merge logic
9270607
@tedil
filter by biotype; keep transcripts with invalid cds when marked as M…
c3b8ffb 
…T*RNA or ProteinCoding
@tedil
remove gene_id→gene_map and map hgnc_id→gene directly instead, less s…
663fbb8 
…ynchronization needed
@tedil
only check cds for protein coding
315d061
@tedil
discard hgnc ids without associated genes (can happen when there are …
5c22ee4 
…transcripts for the hgnc id but no genes in the source files)
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@tedil @holtgrewe