Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / vembrane/vembrane issues and pull requests

#183 - interesting work

Issue - State: closed - Opened by dwpeng 3 months ago

#182 - filter based on fulfilling two out of five conditions

Issue - State: closed - Opened by zihhuafang 4 months ago - 5 comments

#181 - chore: Replace release drafter with release please

Pull Request - State: closed - Opened by tedil 4 months ago

#180 - chore: update project deps for 1.x branch

Pull Request - State: closed - Opened by tedil 4 months ago

#179 - fix: properly handle MATEID presented as single-item

Pull Request - State: closed - Opened by tedil 4 months ago

#178 - fix: properly handle MATEID presented as single-item

Pull Request - State: closed - Opened by tedil 4 months ago

#177 - Update pyproject.toml

Pull Request - State: closed - Opened by christopher-schroeder 4 months ago - 1 comment

#176 - fix: properly handle MATEID presented as single-item

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 1 comment

#175 - Replace release-drafter with release-please

Issue - State: closed - Opened by tedil 5 months ago - 1 comment
Labels: maintenance

#174 - turn docs into a separate page

Issue - State: open - Opened by dlaehnemann 6 months ago - 1 comment

#173 - feat!: Sequence ontology support

Pull Request - State: open - Opened by tedil 6 months ago - 3 comments

#172 - chore: Replace black with ruff

Pull Request - State: closed - Opened by tedil 6 months ago

#171 - vembrane table gives error with multi-sample VCF missing FORMAT entries

Issue - State: closed - Opened by sci-kai 7 months ago - 8 comments

#170 - enhancement: add parsers for SpliceAI and AlphaMissense

Pull Request - State: closed - Opened by tedil 10 months ago

#169 - feat: annotation types for spliceai and alphamissense

Pull Request - State: closed - Opened by FelixMoelder 10 months ago

#168 - Can't install on OSX

Issue - State: closed - Opened by msierk 11 months ago - 1 comment

#165 - Feature: allow intron ranges

Pull Request - State: closed - Opened by christopher-schroeder about 1 year ago

#164 - Custom parser error for INTRON field

Issue - State: closed - Opened by sci-kai about 1 year ago - 2 comments

#163 - feat!: tag, info and ann into annotate

Pull Request - State: open - Opened by christopher-schroeder over 1 year ago

#162 - Add tests for `annotate`

Pull Request - State: open - Opened by tedil over 1 year ago

#161 - v2.0

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

#160 - Multi backend

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

#159 - cyvcf2

Pull Request - State: closed - Opened by christopher-schroeder over 1 year ago - 1 comment
Labels: enhancement

#158 - enhancement: Always report record on error

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

#157 - working info

Pull Request - State: open - Opened by christopher-schroeder over 1 year ago - 3 comments
Labels: enhancement

#156 - Error handling should display the problematic record

Issue - State: closed - Opened by johanneskoester over 1 year ago - 1 comment

#155 - Enhancement: Raise error for filter expressions which do not evaluate to `bool`

Pull Request - State: closed - Opened by tedil over 1 year ago - 7 comments

#154 - please clarify semantics or add check?

Issue - State: closed - Opened by ptrebert over 1 year ago - 3 comments

#151 - v1.0.2 vcf header error

Issue - State: closed - Opened by ptrebert over 1 year ago - 4 comments

#150 - v1.0.2 aux option is broken

Issue - State: closed - Opened by ptrebert over 1 year ago - 8 comments

#149 - Recognize CSQ as ANN

Issue - State: closed - Opened by wwgordon over 1 year ago - 3 comments

#148 - fix: handle missing `ANN`-field for `vembrane table`

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

#147 - feat: Add VCF → SQL/DB functionality

Pull Request - State: open - Opened by tedil over 1 year ago
Labels: enhancement, major

#146 - fix: When a record is missing an entry for ANN, replace with ||||…

Pull Request - State: closed - Opened by tedil almost 2 years ago
Labels: patch

#145 - Update dependencies

Pull Request - State: closed - Opened by tedil almost 2 years ago

#144 - Add testcase for `table --aux`

Pull Request - State: closed - Opened by tedil almost 2 years ago

#143 - Address some mypy errors and hints

Pull Request - State: closed - Opened by tedil almost 2 years ago

#142 - Support `--aux` for vembrane table.

Pull Request - State: closed - Opened by tedil almost 2 years ago

#141 - Fix regex for checking tag names, add more help to tag option

Pull Request - State: closed - Opened by tedil almost 2 years ago
Labels: patch

#140 - Remove deprecated --overwrite-number option

Pull Request - State: closed - Opened by tedil almost 2 years ago

#139 - Introduce `get(item, default=NA)` methods for `INFO`, `ANN` and `FORMAT[field]`

Pull Request - State: closed - Opened by tedil almost 2 years ago - 2 comments
Labels: enhancement, minor

#138 - `PosRange` specific fixes

Pull Request - State: closed - Opened by tedil almost 2 years ago - 1 comment
Labels: patch

#137 - Add '.raw' getter property to custom types to get original annotation string

Pull Request - State: closed - Opened by tedil almost 2 years ago
Labels: minor

#136 - Attribute access on `NA` values results in `NA`

Pull Request - State: closed - Opened by tedil almost 2 years ago
Labels: minor

#135 - No more custom ANN names: always use names from VEP / snpEff as is

Pull Request - State: closed - Opened by tedil almost 2 years ago - 1 comment

#134 - Add support for new-ish gnomADe_* and gnomADg_* entries from VEP

Pull Request - State: closed - Opened by tedil almost 2 years ago - 1 comment

#133 - Update pre commit hook and poetry tool versions

Pull Request - State: closed - Opened by tedil almost 2 years ago

#132 - Add "Citation" section with information on how / what to cite

Pull Request - State: closed - Opened by tedil about 2 years ago

#131 - Slightly better handling of the `##vembraneCmd=…` VCF meta line

Pull Request - State: closed - Opened by tedil over 2 years ago
Labels: patch

#130 - Add examples for working with sample specific values and genotypes

Pull Request - State: closed - Opened by tedil over 2 years ago
Labels: documentation

#128 - feat: support for accessing END position

Pull Request - State: closed - Opened by johanneskoester over 2 years ago

#127 - Improve some type annotations

Pull Request - State: closed - Opened by EQt over 2 years ago

#126 - Add `tag` subcommand

Pull Request - State: closed - Opened by tedil over 2 years ago - 10 comments
Labels: enhancement, major

#125 - Explicitly clear builtins in Environment

Pull Request - State: closed - Opened by tedil over 2 years ago
Labels: patch

#124 - Simplify error types

Pull Request - State: closed - Opened by EQt over 2 years ago
Labels: maintenance

#123 - Mention possibility of `NA` in annotation.

Pull Request - State: closed - Opened by EQt over 2 years ago

#122 - TypeVar instead of Any

Pull Request - State: closed - Opened by EQt over 2 years ago

#121 - Some documentation improvements

Pull Request - State: closed - Opened by EQt over 2 years ago

#119 - return NA in case of MISSING (".") ALT

Pull Request - State: closed - Opened by tedil over 2 years ago
Labels: patch

#118 - Print the record itself in addition to the record index when encountering exceptions

Pull Request - State: closed - Opened by tedil over 2 years ago
Labels: maintenance

#117 - Make black and isort work together nicely

Pull Request - State: closed - Opened by tedil over 2 years ago
Labels: maintenance

#116 - Minor formatting/Sort imports

Pull Request - State: closed - Opened by EQt over 2 years ago - 2 comments
Labels: maintenance

#115 - Allow comparisons to `InfoTuple`

Pull Request - State: closed - Opened by tedil over 2 years ago
Labels: patch

#114 - Allow tidy table / long format tsv output

Pull Request - State: closed - Opened by tedil over 2 years ago - 4 comments

#113 - Do not output records unconditionally when `--preserve-order` is activated

Pull Request - State: closed - Opened by tedil over 2 years ago

#112 - `--overwrite-number` fixes and pysam special treatment

Pull Request - State: closed - Opened by tedil over 2 years ago - 1 comment

#111 - Replace float constants in expressions with IEEE-754-1985 32bit float constants.

Pull Request - State: closed - Opened by tedil over 2 years ago - 5 comments
Labels: minor

#110 - Change backend from `pysam` to `cyvcf2`

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

#109 - docs: add `ID` to list of available fields in README.md

Pull Request - State: closed - Opened by dlaehnemann over 2 years ago

#108 - pyproject.toml adjustments, bump patch version

Pull Request - State: closed - Opened by tedil over 2 years ago
Labels: patch

#107 - Update numpy version (to address dependabot warning)

Pull Request - State: closed - Opened by tedil over 2 years ago
Labels: minor

#106 - Enable `--overwrite-number` option for table subcommand as well

Pull Request - State: closed - Opened by tedil over 2 years ago
Labels: patch

#105 - Exact filtering in FILTER column

Issue - State: closed - Opened by kokyriakidis over 2 years ago - 5 comments

#104 - Add `without_na`, `replace_na` and common functions from python's `statistics` module

Pull Request - State: closed - Opened by tedil over 2 years ago - 2 comments
Labels: minor

#103 - fix: add test case to cover ANN['EXON'] fields with a range like `4-6/27`

Pull Request - State: closed - Opened by dlaehnemann over 2 years ago - 3 comments
Labels: minor

#102 - Add more annotation types

Pull Request - State: closed - Opened by dlaehnemann almost 3 years ago - 1 comment

#101 - Fix subsequent ALT accesses yielding list not str

Pull Request - State: closed - Opened by mbargull over 3 years ago
Labels: bug

#100 - Fix tests to check all expected entries/headers

Pull Request - State: closed - Opened by mbargull over 3 years ago
Labels: maintenance

#99 - GT 1/1 Error

Issue - State: closed - Opened by christopher-schroeder over 3 years ago - 3 comments

#98 - Annotate

Pull Request - State: closed - Opened by christopher-schroeder over 3 years ago - 1 comment
Labels: enhancement, help wanted, major

#97 - support BCF files in the testing harness

Issue - State: open - Opened by dlaehnemann almost 4 years ago

#96 - A flag should be a single boolean value, not a tuple with 1 entry

Pull Request - State: closed - Opened by tedil almost 4 years ago
Labels: bug

#95 - fix and test table args handling

Pull Request - State: closed - Opened by dlaehnemann almost 4 years ago - 16 comments
Labels: bug, documentation, enhancement

#94 - Add __len__ to InfoTuple

Pull Request - State: closed - Opened by tedil almost 4 years ago

#93 - Better handling of Number=1 and NoValue

Pull Request - State: closed - Opened by tedil almost 4 years ago - 1 comment

#92 - Implement `hash` for NoValue

Pull Request - State: closed - Opened by tedil about 4 years ago

#91 - Add option for auxiliary files containing sets of symbols

Pull Request - State: closed - Opened by tedil about 4 years ago

#90 - Format containment fix

Pull Request - State: closed - Opened by tedil about 4 years ago
Labels: patch

#89 - Allow indexed table

Pull Request - State: closed - Opened by christopher-schroeder about 4 years ago
Labels: enhancement, patch

#88 - Add --version option

Pull Request - State: closed - Opened by tedil about 4 years ago

#87 - Custom functions

Pull Request - State: closed - Opened by tedil over 4 years ago

#86 - Proper repr and str methods, might break 'vembrane table'?

Pull Request - State: closed - Opened by tedil over 4 years ago

#85 - Custom functions

Pull Request - State: closed - Opened by tedil over 4 years ago - 15 comments

#84 - More custom VEP annotation types

Pull Request - State: closed - Opened by tedil over 4 years ago
Labels: patch