openvax/varcode issues and pull requests

#253 - Defaulting convert_ucsc_contig_names to True for consistency with past behavior

Pull Request - State: closed - Opened by julia326 about 1 year ago - 3 comments

#252 - Add variant and effect classes for gene fusions

Issue - State: open - Opened by iskandr over 1 year ago

#251 - Fix error of transcript name

Pull Request - State: closed - Opened by y9c over 1 year ago

#250 - Insertion effect from SNV?

Issue - State: open - Opened by iskandr almost 2 years ago - 1 comment

#249 - Update varcode in PyPI

Issue - State: closed - Opened by jonasscheid over 2 years ago - 2 comments

#248 - No module named 'pyensembl.biotypes'

Issue - State: closed - Opened by LisaMMilchsack over 3 years ago

#247 - pyvcf dependency is causing installation failure on setuptools>=58

Issue - State: open - Opened by susannasiebert almost 4 years ago - 4 comments

#246 - error on nonframeshift deletion

Issue - State: open - Opened by mpallocc over 5 years ago - 1 comment

#245 - Fix reference names from CLI

Pull Request - State: closed - Opened by iskandr over 5 years ago - 1 comment

#244 - added keyword aliases to Variant

Pull Request - State: closed - Opened by iskandr almost 6 years ago - 1 comment

#243 - Make liftover between genomes explicit method

Issue - State: open - Opened by iskandr almost 6 years ago

#242 - Correct handling of UCSC vs. Ensembl reference genomes

Pull Request - State: closed - Opened by iskandr almost 6 years ago - 3 comments

#241 - Incorrect normalization of "chrM" on GRCh38 to "MT"

Issue - State: closed - Opened by iskandr almost 6 years ago - 1 comment

#240 - default sequence length to 0 if None during effect ordering

Pull Request - State: closed - Opened by iskandr almost 6 years ago - 1 comment

#239 - Encountered error during effect sorting due to empty sequence

Issue - State: closed - Opened by iskandr almost 6 years ago

#238 - Incorrect result (and fix) in effect_ordering.py

Issue - State: closed - Opened by LouieKam about 6 years ago - 3 comments

#237 - Smarter selection of top priority effect

Pull Request - State: closed - Opened by iskandr over 6 years ago - 1 comment

#236 - WT and mutation AA incorrect for variant in codon split across exon boundary

Issue - State: closed - Opened by ijhoskins over 6 years ago - 12 comments

#235 - fixed top_priority_effect for ExonicSpliceSite

Pull Request - State: closed - Opened by iskandr almost 7 years ago - 1 comment

#234 - varcode on Windows throws error: ImportError: No module named 'resource'

Issue - State: closed - Opened by 229668880 almost 7 years ago - 4 comments

#233 - Consider alternative effect of ExonicSpliceSite for "top priority"

Issue - State: closed - Opened by iskandr almost 7 years ago

#232 - added --download-reference-genome-data command

Pull Request - State: closed - Opened by iskandr almost 7 years ago - 1 comment

#231 - Add CLI option to automatically run PyEnsembl install()

Issue - State: closed - Opened by iskandr almost 7 years ago - 1 comment

#230 - Test gtfparse==0.0.6 fixed version

Pull Request - State: closed - Opened by iskandr over 7 years ago

#229 - Add a `difference` set operation to VariantCollection

Issue - State: open - Opened by julia326 over 7 years ago

#228 - small fixes to code formatting

Pull Request - State: closed - Opened by iskandr over 7 years ago - 1 comment

#227 - EffectCollection is not sorted by priority by default

Issue - State: open - Opened by tavinathanson almost 8 years ago
Labels: bug

#226 - WIP: Basic VCF output functionality, given a single variant source.

Pull Request - State: closed - Opened by jlkravitz about 8 years ago - 10 comments

#225 - Adding a logging statement when trimming a variant to match an exon

Pull Request - State: closed - Opened by julia326 about 8 years ago - 1 comment

#224 - Exception when deletion extends beyond exon boundary

Issue - State: closed - Opened by iskandr about 8 years ago - 4 comments

#223 - Fixes to load_maf

Pull Request - State: closed - Opened by tavinathanson over 8 years ago - 2 comments

#222 - Adding 'distinct' as a parameter to load_vcf.

Pull Request - State: closed - Opened by julia326 over 8 years ago - 2 comments

#221 - added raise_on_error option to load_maf and load_maf_dataframe

Pull Request - State: closed - Opened by iskandr over 8 years ago - 3 comments

#220 - Order of VariantCollection with sort_key=None

Issue - State: open - Opened by iskandr over 8 years ago - 1 comment

#219 - install ensembl 87 on travis

Pull Request - State: closed - Opened by iskandr over 8 years ago - 2 comments

#218 - Allow user to affect the sorting of variants when loading a VCF or MAF.

Pull Request - State: closed - Opened by tuomastik over 8 years ago - 3 comments

#217 - Use HGVS format for Silent.short_description

Issue - State: open - Opened by joaoe over 8 years ago

#216 - Fix short_description for PrematureStop with empty aa_ref

Issue - State: open - Opened by joaoe over 8 years ago - 1 comment

#215 - What if the ref allele is a common SNP?

Issue - State: open - Opened by johannesreiter over 8 years ago - 4 comments

#214 - Allow specification of ensembl release as part of genome on commandline

Issue - State: open - Opened by iskandr over 8 years ago

#213 - Effect prediction throws error (even if raise_on_error=False)

Issue - State: closed - Opened by johannesreiter over 8 years ago - 2 comments

#212 - Optionally allow duplicated mutations when using load_vcf or load_maf. Fixes #211

Pull Request - State: closed - Opened by tuomastik over 8 years ago - 8 comments

#211 - Optionally allow duplicated mutations when using load_vcf or load_maf

Issue - State: closed - Opened by tuomastik over 8 years ago - 2 comments

#210 - Allow contig to be empty to allow parsing of MAF with faulty mutation(s)

Issue - State: closed - Opened by tuomastik over 8 years ago - 5 comments

#209 - Add optional_cols list to load_maf

Pull Request - State: closed - Opened by tavinathanson over 8 years ago - 1 comment

#208 - Silent.aa_pos wrong for synonymous SNPs

Issue - State: open - Opened by joaoe over 8 years ago - 1 comment

#207 - Make Varcode correctly infer genome for b37-decoy string

Issue - State: closed - Opened by julia326 over 8 years ago - 3 comments

#206 - Provide mutation info with StartLosses

Issue - State: open - Opened by joaoe over 8 years ago - 1 comment

#205 - Stoploss confused as insert

Issue - State: open - Opened by joaoe over 8 years ago

#204 - WIP: Fixes silent insertion before stop codon being labeled as "Insertion"

Pull Request - State: closed - Opened by iskandr over 8 years ago - 1 comment

#203 - Adding aa_ref argument to StopLoss for variants which delete codons before stop

Pull Request - State: closed - Opened by iskandr over 8 years ago - 2 comments

#202 - Variants before and over the stop codon lose information.

Issue - State: closed - Opened by joaoe over 8 years ago - 2 comments

#201 - Synonymous Insertion before stop codon annotated as non silent insert

Issue - State: open - Opened by joaoe almost 9 years ago - 2 comments

#200 - Varcode noncoding variant in a drop_silent_and_noncoding() list

Issue - State: closed - Opened by ihodes almost 9 years ago - 2 comments
Labels: bug

#199 - explicit args to init of Intronic splice effects fixes serialization

Pull Request - State: closed - Opened by iskandr almost 9 years ago - 3 comments

#198 - Update RELEASING.md, fixing tagging instructions

Pull Request - State: closed - Opened by julia326 almost 9 years ago - 4 comments

#197 - One logger per module.

Pull Request - State: closed - Opened by julia326 almost 9 years ago - 3 comments

#196 - One logger per module

Issue - State: closed - Opened by julia326 almost 9 years ago

#195 - Annotate all transcripts

Issue - State: open - Opened by joaoe almost 9 years ago - 4 comments

#194 - Fix edge case where PrematureStop in last amino acid got interpreted as a Deletion

Pull Request - State: closed - Opened by iskandr almost 9 years ago - 2 comments

#193 - SNV results in deletion

Issue - State: closed - Opened by arahuja almost 9 years ago - 2 comments

#192 - changed Markdown image links to HTML

Pull Request - State: closed - Opened by iskandr almost 9 years ago - 5 comments

#191 - Link on PyPI badge broken

Issue - State: closed - Opened by iskandr almost 9 years ago

#190 - Move extraneous variables to properties for normalization

Pull Request - State: closed - Opened by tavinathanson almost 9 years ago - 1 comment

#189 - Use conda to install pypandoc

Pull Request - State: closed - Opened by arahuja almost 9 years ago - 1 comment

#188 - StopLoss pickling is broken

Issue - State: closed - Opened by tavinathanson almost 9 years ago - 2 comments
Labels: bug

#187 - Installation of varcode requires README.md

Issue - State: open - Opened by iskandr almost 9 years ago - 1 comment

#186 - Ensure README.md is packaged

Pull Request - State: closed - Opened by arahuja almost 9 years ago - 1 comment

#185 - Upgrade serializable dependency with tests

Pull Request - State: closed - Opened by arahuja almost 9 years ago - 2 comments

#184 - Add pypi badge

Pull Request - State: closed - Opened by arahuja almost 9 years ago - 2 comments

#183 - Import of varcode is slow

Issue - State: closed - Opened by joaoe almost 9 years ago - 3 comments

#182 - Fix inferred-reference-bug

Pull Request - State: closed - Opened by jburos almost 9 years ago - 13 comments

#181 - Reference incorrectly inferred when "b36" in reference file path

Issue - State: closed - Opened by jburos almost 9 years ago

#180 - Use is_protein_coding property of pyensembl.Transcript and pyensembl.Gene

Pull Request - State: closed - Opened by iskandr almost 9 years ago - 2 comments

#179 - Variant effects should contain mutated_sequence

Issue - State: open - Opened by ihodes almost 9 years ago - 2 comments
Labels: enhancement

#178 - Add MutationEffect to init.py

Pull Request - State: closed - Opened by timodonnell almost 9 years ago - 4 comments

#177 - README formatting messed up on PyPI

Issue - State: closed - Opened by iskandr almost 9 years ago - 1 comment

#176 - Substitution mis-annotated as stop-loss

Issue - State: closed - Opened by iskandr almost 9 years ago - 1 comment

#175 - Wrong aa_mutation_end_offset for insertion of stop codon

Issue - State: closed - Opened by iskandr almost 9 years ago - 3 comments

#174 - Wrong aa_ref for insertion of stop codon

Issue - State: closed - Opened by iskandr almost 9 years ago - 1 comment