biocommons hgvs issues - Githubissues

biocommons / hgvs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

https://hgvs.readthedocs.io/

Apache License 2.0

233 stars 94 forks source link

issues

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#744 - babelfish vcf conversion accept contig accessions as chrom names

#745 davmlaw closed 6 days ago
1
babelfish VCF to g.HGVS fails when contig accession used as chromosome name

#744 davmlaw closed 6 days ago
0
Is it possible to get hgvs official name from "15-49716528-A-G"？

#743 shizipo opened 1 week ago
1
feat(#741): Pretty print

#742 andreasprlic opened 3 weeks ago
1
Context view improvements

#741 andreasprlic opened 3 weeks ago
2
style: format with Ruff

#740 jsstevenson opened 3 weeks ago
2
build: require python >= 3.10

#739 jsstevenson opened 3 weeks ago
1
refactor: use importlib instead of pkg_resources

#738 jsstevenson closed 1 month ago
0
chore: remove trailing whitespace

#737 jsstevenson closed 1 month ago
1
Global configuration item not always being used

#736 wlymanambry opened 2 months ago
0
Support transcript identifiers (in parentheses) in variants

#735 marius-mather opened 2 months ago
0
feat: update default data version config

#734 jsstevenson closed 2 months ago
5
Update default config to uta v20210129b?

#733 larrybabb closed 2 months ago
0
CDS phase (frame offset for eg ribo slippage) not taken into account in amino acid translation

#732 davmlaw opened 3 months ago
0
#730 - Fix single letter amino acid bug

#731 jPleyte closed 3 months ago
1
For start loss AARefAlt.format always returns 3 letter amino acid even when single letter amino acid is configured

#730 jPleyte closed 3 months ago
0
#178 - use abc for Edit class to ensure method definition

#729 davmlaw closed 3 months ago
2
#695 - Remove top level code environment scripts from modules

#728 davmlaw closed 4 months ago
0
p type cannot be validated

#727 markgene opened 4 months ago
1
#688 - remove __future__ usage

#726 davmlaw closed 4 months ago
0
fix: update gene symbol when it is `None` and `AssemblyMapper` normalizer

#725 markgene closed 1 month ago
4
`g_to_t` for promoter regions

#724 markgene closed 4 months ago
2
#722 Babelfish VCF bugs

#723 davmlaw closed 3 months ago
3
Babelfish vcf conversion errors - case sensitivity, multi-base identities

#722 davmlaw closed 3 months ago
1
Investigate and improve hgvs performance

#721 reece closed 1 month ago
2
Modify parser to include common errors to provide better error messages than "syntax error"

#720 davmlaw opened 5 months ago
3
Fix ins or dups where splice region is preserved

#719 b0d0nne11 opened 5 months ago
9
Problems hgvs between build 37 and 38

#718 jeantristanb closed 5 months ago
4
Coordinate is out of bounds error when roundtripping GRCh38 variants via `g_to_c` + `c_to_g` and `relevant_transcripts`

#717 mihaitodor closed 5 months ago
5
Add variant region condition for dups ending in UTR

#716 b0d0nne11 closed 3 weeks ago
3
c_to_p for dups that start in transcript but end in UTR

#715 b0d0nne11 closed 3 weeks ago
10
c_to_p at intron/exon boundary where splice region is preserved

#714 b0d0nne11 opened 6 months ago
3
fix(#712): This fixes the broken make develop install

#713 andreasprlic closed 6 months ago
1
make develop not working

#712 andreasprlic closed 6 months ago
1
Consider exposing a utility for converting between g. variants by leveraging pyliftover

#711 mihaitodor opened 7 months ago
6
How to properly handle selenoproteins

#710 holtgrewe opened 7 months ago
3
Fix variant region for ins and dup on intron-exon boundary

#709 b0d0nne11 opened 8 months ago
15
fix: projection issue for stop retained insertion (#707)

#708 holtgrewe opened 8 months ago
11
hgvs_c to hgvs_p projection throws IndexError for "NM_001253909.2:c.416_417insGTG"

#707 holtgrewe opened 8 months ago
2
Validation - refactor to be able to retrieve all errors rather than throw exception on 1st

#706 davmlaw opened 8 months ago
5
`Normalizer.normalize()` is performing sequence position validation which cannot be skipped

#705 mihaitodor opened 8 months ago
4
Normalizer constructor doesn't pass the `validate` param to the VariantMapper constructor

#704 mihaitodor opened 8 months ago
4
Liftover hgvs nomenclature from hg19 to hg38

#703 vlakhujani closed 9 months ago
1
#701 - Add name to metadata

#702 davmlaw closed 6 months ago
3
setup.cfg metadata

#701 davmlaw closed 5 months ago
2
Exon boundary / intron validation - need for genome build specific validation?

#700 davmlaw opened 9 months ago
4
Uncertain ranges

#699 theferrit32 opened 9 months ago
19
Add python runner

#698 Estefanos8080 closed 4 months ago
7
Remove test HTTP network calls

#697 ecalifornica closed 9 months ago
0
Remove top level code environment script

#696 ecalifornica closed 9 months ago
0