Whats wrong with variant application and xml - #956

Closed

trishorts wants to merge 140 commits into

smith-chem-wisc:masterfrom

trishorts:whatsWrongWithVariantApplicationAndXml

Commits on Sep 17, 2025

d
trishorts
committed
650f2fa
its broke
trishorts
committed
132b6ca
string unneccessary lines from xml
trishorts
committed
aed5b13

Commits on Sep 22, 2025

nucleotide substitution modifications converted to squence variants during read
trishorts
committed
71543b0
correctly set max variants per isoform and max isoform variants with unit tests
trishorts
committed
3f90baf
still trouble correctly handling VCF sequence variants
trishorts
committed
312a385

Commits on Sep 24, 2025

add extensive comments to SequenceVariantDescription
trishorts
committed
197a4f8

Commits on Sep 25, 2025

Commits on Sep 26, 2025

new code that splits sequence variants by genotypes and new code that combines sequence variants with the same effect
trishorts
committed
6ca8a19
we now have one method to apply all variants
trishorts
committed
7f94034
fixed vcf constructor test
trishorts
committed
6da8776
slow progress
trishorts
committed
941da42
increment
trishorts
committed
84dc0a8
IndelDecoyVariants passes
trishorts
committed
f7e3c7e
multiple alternate alleles passes
trishorts
committed
5c391e5
multiple alternate frameshifts passes
trishorts
committed
ffd6c5c
stop gained passes
trishorts
committed
f83491b

Commits on Sep 30, 2025

stable
trishorts
committed
fab8922
fixed homozygous variants
trishorts
committed
31d430b
load seq var mods fixed
trishorts
committed
dfbcb66
variant symbol weirdness fixed
trishorts
committed
3d3f335
VariantXml fixed
trishorts
committed
d94c9d7
one more variant depth change
trishorts
committed
3507d55
test full protein read write fixed
trishorts
committed
c193b50
RNA two truncations fixed
trishorts
committed
2106390
b
trishorts
committed
18ddc71
applied variants fixed
trishorts
committed
d41b4b3
indel decoy variants
trishorts
committed
5533480
multiple alternate alleles
trishorts
committed
8557e13
stop gained
trishorts
committed
bc074dc
variantxml
trishorts
committed
96e5ca2
homozygous variants
trishorts
committed
40927bc
load seq var
trishorts
committed
b44837d
test identify and string
trishorts
committed
ccce660
test hash
trishorts
committed
fd8c528
compare protein properties
trishorts
committed
34572ad
testing comlete xmls
trishorts
committed
43d3b85
progress
trishorts
committed
c685909
no progress
trishorts
committed
7dfa78c
before changes to proteindbwriter
trishorts
committed
6fea76c
okay don't sneeze
trishorts
committed
b7c725f

Commits on Oct 1, 2025

is this even real
trishorts
committed
4a6a4b7
better
trishorts
committed
0fa3981
n
trishorts
committed
d2e38eb
f
trishorts
committed
2902d61
dont sneeze bro
trishorts
committed
8921cd0
intersects sequence variations
trishorts
committed
5e8a6e4
test hash fixed
trishorts
committed
f82ba62
applied variants as i biopolymer
trishorts
committed
b1219b6
indel decoy
trishorts
committed
3243e32
g
trishorts
committed
41b439d
cool
trishorts
committed
a8c8207
green light baby
trishorts
committed
cfb9dcc
Merge remote-tracking branch 'upstream/master' into whatsWrongWithVariantApplicationAndXml
trishorts
committed
15fe961

Commits on Oct 2, 2025

sentize variants test start
trishorts
committed
a4ca06d
sanitize variant data test complete
trishorts
committed
0e1431c
combine descriptions unit test
trishorts
committed
3114199
test nucleotide substitution modification to sequence variant
trishorts
committed
7142dc0
variant application tests
trishorts
committed
7d60e22
nice
trishorts
committed
3ece78d
apply variants tests
trishorts
committed
3a24d34
sanitize start
trishorts
committed
171ac85
k
trishorts
committed
d623db1
good
trishorts
committed
ff07a18
good
trishorts
committed
7941caf
sanitize covered
trishorts
committed
1ed8f2a
mid
trishorts
committed
0e0ebd6
get biopolymers comprehensive tests
trishorts
committed
932a854
truncation product tests
trishorts
committed
7a6a325
test sequence variation indicies
trishorts
committed
b12abbf
test apply single variant
trishorts
committed
ab986ac
split per genotype tests begin
trishorts
committed
1b2bd69
split per genotypes tests complete
trishorts
committed
33690ac
eliminate unused code in SnpEffAnnotation
trishorts
committed
e9a4482
put it back
trishorts
committed
7f3c68c

Commits on Oct 3, 2025

Commits on Oct 6, 2025

fix copilot reported issues
trishorts
committed
56a1cee
dbloader tests
trishorts
committed
4ae1030
additional sequence variation tests
trishorts
committed
6702ad7

Commits on Oct 7, 2025

peptide with set mods tests
trishorts
committed
7842e09

Commits on Oct 9, 2025

j
trishorts
committed
48575d6
fix unit tests that broke because of differences in the order that proteins were written
trishorts
committed
7739a00
its cool
trishorts
committed
c1e8ee9
updates to make rna db writer consistant w/ protein db writer
trishorts
committed
13b7ba9
i dont believe that it actually works
trishorts
committed
2f7a061
correctly write proteins with applied variants
trishorts
committed
2325fde
collapse proteins with the same accession derived from application of variants
trishorts
committed
68dabc2
test collapse proteins with applied variants having the same accession during db read
trishorts
committed
814c193
change LoadProteinXML defaults so no variants get loaded by default and adjust unit tests accordingly
trishorts
committed
d4a2ebb
fix more unit tests that fail due to changes in the default values
trishorts
committed
fc3b55a
repair more broken unit tests
trishorts
committed
ec85f4c
no beta
trishorts
committed
33d10e6
plus four
trishorts
committed
9076e5d
yay
trishorts
committed
db5b313
h
trishorts
committed
bf9ae07
amended default to return canonical in proteindbreader
trishorts
committed
a1eb4a0

Commits on Oct 13, 2025

lots of updates for decoys of proteins with sequence variants
trishorts
committed
3261850
delete unused code
trishorts
committed
fc87bc9

Commits on Oct 14, 2025

f
trishorts
committed
75c0631
g
trishorts
committed
dd07eaf
stuff is working
trishorts
committed
b115053

Commits on Oct 15, 2025

gs
trishorts
committed
b500d86
remove local reference
trishorts
committed
af61107

Commits on Oct 20, 2025

extend variant application changes to rna and writing and reading of such
trishorts
committed
895766f
test rna with truncation
trishorts
committed
4f9d714
update xmlentry and dbloader to read decoys
trishorts
committed
060a244
x
trishorts
committed
abc110d
intermediate save
trishorts
committed
4c96cbc
keep organism is merge proteins
trishorts
committed
f2a8c82
manually merged nics decoy stuff
trishorts
committed
4726017
merge upstream
trishorts
committed
c2c3f05
nics stuff is in
trishorts
committed
966a65a
legacy load protein xml
trishorts
committed
9c52cee

Commits on Oct 21, 2025

test for convert nucleotide substitution mod in loadproteinxml
trishorts
committed
2aa7a09
test legacy loadproteinxml
trishorts
committed
2c8c0ba
covering some variant lines in peptide with set mods
trishorts
committed
136225c
update nuspec
trishorts
committed
b06ed98
organization
trishorts
committed
1020526
Merge remote-tracking branch 'upstream/master' into whatsWrongWithVariantApplicationAndXml
trishorts
committed
085116c

Commits on Oct 22, 2025

j
trishorts
committed
4319338
tests
trishorts
committed
c4d52e8
okay so peptide with set mods intersects was bugged
trishorts
committed
8292548
ok cool
trishorts
committed
0618dce
unused code
trishorts
committed
a2eb07c
summary comments
trishorts
committed
663d07e
g
trishorts
committed
01b9de2
comments
trishorts
committed
6029fda
Merge remote-tracking branch 'upstream/master' into whatsWrongWithVariantApplicationAndXml
trishorts
committed
d90c2de
return comments to snpeff
trishorts
committed
ed48f63
rename maxIsoforms
trishorts
committed
4dfbd11
better not perfect
trishorts
committed
3d73744