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fix: refactor csq analysis code #599

Merged
merged 38 commits into from
Nov 19, 2024
Merged

fix: refactor csq analysis code #599

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9eb5000
chore: refactor csq analysis code
tedil Nov 4, 2024
aa23589
more refactoring + move *_inframe_deletion detection to var_c (from v…
tedil Nov 4, 2024
7bbe60a
update cargo lock
tedil Nov 5, 2024
60811b1
alias BitFlags<Consequence> to Consequences
tedil Nov 5, 2024
40c4b2c
undo: move inframedeletion to var_c (from var_p)
tedil Nov 5, 2024
dccb09e
lints
tedil Nov 5, 2024
b97b650
if let instead of match
tedil Nov 5, 2024
5504862
fix gained vs lost typo
tedil Nov 5, 2024
0f71645
remove multiple intron_start matches
tedil Nov 5, 2024
2a84229
move intron_start check out of fn
tedil Nov 5, 2024
5a80949
don't overwrite previous consequences, union instead
tedil Nov 5, 2024
ebdbd51
update cargo lock
tedil Nov 5, 2024
81e8e2f
lint
tedil Nov 5, 2024
68fef4b
check for StopRetained based on DelIns length agreement with loc edit
tedil Nov 6, 2024
d41d205
merge origin/dev
tedil Nov 12, 2024
87d9f13
consider feature elongation
tedil Nov 12, 2024
5cad620
re-check start codon modifications
tedil Nov 12, 2024
e44ee30
use cmp and match
tedil Nov 12, 2024
68d9fb4
re-establish accidentally deleted inframedeletion csq
tedil Nov 12, 2024
31bffd6
remove superfluous prefix
tedil Nov 12, 2024
91d6c0e
account for cds change not starting at 1
tedil Nov 12, 2024
a110015
extract has_stop method
tedil Nov 12, 2024
c14f746
only undo stoplost when stopretained
tedil Nov 12, 2024
29c8ef2
fix parentheses
tedil Nov 12, 2024
39c64d9
tidy up vep/snpeff comparison fixing code slightly
tedil Nov 12, 2024
e6be328
add specific test for vep reporting coding_sequence_variant only
tedil Nov 12, 2024
bd69c9e
detangle intronic and exonic variant csq logic
tedil Nov 14, 2024
968cbb4
move more exon specific code into analyze_exonic_variant
tedil Nov 14, 2024
a80e336
update snapshots
tedil Nov 14, 2024
13d7a4e
be a bit more careful when it comes to frameshifts
tedil Nov 15, 2024
0259fad
uncomment last change for now
tedil Nov 15, 2024
ec20820
move fs*2 handling to special case function
tedil Nov 18, 2024
cdc4e77
clippy lint
tedil Nov 18, 2024
0d481e2
update comment
tedil Nov 18, 2024
9837b9a
be more strict regarding start_retained
tedil Nov 18, 2024
536bc7e
add todo regarding other cases (e.g. ins)
tedil Nov 18, 2024
b62d629
added testcase for vep←→ mehari disagreement cases
tedil Nov 18, 2024
7f12193
added testcase for vep←→ mehari disagreement cases
tedil Nov 18, 2024
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