Ecosyste.ms: Issues

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

GitHub / bioinfo-chru-strasbourg/howard issues and pull requests

#273 - Export only prioritize transcript annotation

Issue - State: closed - Opened by JbaptisteLam 5 months ago - 2 comments
Labels: improve

#272 - Error in prioritization step

Issue - State: closed - Opened by JbaptisteLam 5 months ago - 1 comment
Labels: bug

#271 - Add option only_info #268, docs #4

Pull Request - State: closed - Opened by antonylebechec 5 months ago

#270 - Query tool - disable output print

Issue - State: closed - Opened by antonylebechec 5 months ago - 1 comment
Labels: improve

#269 - improve type for dbnsfp databases #268, and improve tests

Pull Request - State: closed - Opened by antonylebechec 5 months ago

#268 - Improve type for dbNSFP

Issue - State: closed - Opened by antonylebechec 5 months ago - 2 comments
Labels: improve

#266 - Annotation file not found

Issue - State: closed - Opened by JbaptisteLam 6 months ago - 1 comment
Labels: improve

#265 - Add prioritization in SQL format

Issue - State: closed - Opened by antonylebechec 6 months ago - 2 comments
Labels: improve

#264 - Improve samples identification

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

#263 - Manage sample columns in input file

Issue - State: closed - Opened by antonylebechec 6 months ago - 2 comments
Labels: improve

#262 - Add INFO annotations for transcripts prioritization #256

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

#261 - Sample columns disappear

Issue - State: closed - Opened by JbaptisteLam 6 months ago - 1 comment
Labels: bug

#260 - Transcript bubble view

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

#259 - Transcript bubble view

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

#258 - GA4GH compatibility

Issue - State: open - Opened by antonylebechec 6 months ago
Labels: enhancement, improve

#257 - Transcript bubble view

Pull Request - State: closed - Opened by antonylebechec 7 months ago

#256 - Add transcripts level

Issue - State: closed - Opened by antonylebechec 7 months ago - 11 comments
Labels: enhancement

#255 - Add uniquify option on dbNSFP database generation #254

Pull Request - State: closed - Opened by antonylebechec 7 months ago

#254 - Add uniquify option for dbNSFP database generation

Issue - State: closed - Opened by antonylebechec 7 months ago - 1 comment
Labels: enhancement

#253 - Change calculation names and options #11

Pull Request - State: closed - Opened by antonylebechec 7 months ago

#252 - Add snpEff ANN split into multiple fields #11

Pull Request - State: closed - Opened by antonylebechec 7 months ago

#251 - 0.11.0

Pull Request - State: closed - Opened by antonylebechec 7 months ago

#250 - fix splice #192, docs #4 and tests

Pull Request - State: closed - Opened by antonylebechec 7 months ago

#249 - Add docs #4 for splice tool

Pull Request - State: closed - Opened by antonylebechec 7 months ago

#248 - fix snpeff download when databases list is empty #244

Pull Request - State: closed - Opened by antonylebechec 7 months ago

#247 - Fix splice

Pull Request - State: closed - Opened by antonylebechec 7 months ago

#246 - howard convert error

Issue - State: closed - Opened by JbaptisteLam 7 months ago - 1 comment

#245 - Splice

Pull Request - State: closed - Opened by antonylebechec 8 months ago

#244 - Auto remove snpEff databases list when empty

Issue - State: closed - Opened by antonylebechec 8 months ago - 2 comments
Labels: bug

#243 - Fix genomes folder and genome invalid path error

Pull Request - State: closed - Opened by antonylebechec 8 months ago - 1 comment

#242 - Fix genomes folder invalid path #240

Pull Request - State: closed - Opened by antonylebechec 8 months ago

#241 - Update packages

Pull Request - State: closed - Opened by antonylebechec 8 months ago

#240 - Not able to download databases

Issue - State: closed - Opened by zuber-bioinfo 8 months ago - 8 comments

#239 - Omim annotation issue : gene list not sorted

Issue - State: closed - Opened by Melalaoua 9 months ago - 2 comments
Labels: bug

#238 - Potential Python Version Dependency Issue (Resolved)

Issue - State: closed - Opened by judefelixt 9 months ago - 2 comments

#237 - 0.10.0

Pull Request - State: closed - Opened by antonylebechec 9 months ago

#236 - Add snpsift

Pull Request - State: closed - Opened by antonylebechec 9 months ago

#235 - Add snpsift

Pull Request - State: closed - Opened by antonylebechec 9 months ago

#234 - Add quick annotation for each specific tool/method

Issue - State: closed - Opened by antonylebechec 9 months ago - 1 comment
Labels: enhancement

#233 - Add snpSift annotation tool

Issue - State: closed - Opened by antonylebechec 9 months ago - 1 comment
Labels: enhancement

#232 - Fix export variant vcf

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

#231 - Error while exporting variant into vcf

Issue - State: closed - Opened by JbaptisteLam 10 months ago - 2 comments
Labels: bug

#230 - Add barcode family #229, and some fixes

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

#229 - Add barcode on genotype for a family

Issue - State: closed - Opened by antonylebechec 10 months ago - 1 comment
Labels: enhancement

#227 - Clean annotation parquet

Issue - State: closed - Opened by antonylebechec 10 months ago - 1 comment
Labels: improve, clean

#226 - Clean SonarLint issues

Issue - State: open - Opened by antonylebechec 10 months ago
Labels: clean

#225 - fix from annovar tool #224

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

#224 - Fix from_annovar with wrong header calculation

Issue - State: closed - Opened by antonylebechec 10 months ago - 1 comment
Labels: bug

#223 - fix #221

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

#222 - update polars, remove header file for VCF #221

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

#221 - Remove export header when output format is VCF

Issue - State: closed - Opened by antonylebechec 10 months ago - 1 comment
Labels: bug

#220 - Fix sort memory issue

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

#219 - Fix parquet partition option

Issue - State: closed - Opened by antonylebechec 10 months ago - 1 comment
Labels: bug

#218 - Error when VCF sort for huge file

Issue - State: closed - Opened by antonylebechec 10 months ago - 1 comment
Labels: bug

#217 - Fix database header export vcf extra columns

Pull Request - State: closed - Opened by antonylebechec 11 months ago

#216 - Ensure VCF columns are samples with well formed genotype

Issue - State: closed - Opened by antonylebechec 11 months ago - 1 comment
Labels: bug

#215 - Fix bad header error not shown

Issue - State: closed - Opened by antonylebechec 11 months ago - 1 comment
Labels: bug

#214 - Options and docs

Pull Request - State: closed - Opened by antonylebechec 11 months ago

#213 - fix param_extann option

Pull Request - State: closed - Opened by antonylebechec 11 months ago

#212 - docs #4 with html and PDF

Pull Request - State: closed - Opened by antonylebechec 11 months ago

#207 - Add plugins module

Issue - State: closed - Opened by antonylebechec 11 months ago - 1 comment
Labels: enhancement

#192 - Add splice annotation

Issue - State: closed - Opened by antonylebechec 11 months ago - 1 comment
Labels: enhancement

#190 - Add Gene annotation database generation

Issue - State: closed - Opened by antonylebechec 11 months ago - 1 comment
Labels: enhancement

#154 - Trouble while using BED as annotation file

Issue - State: closed - Opened by JbaptisteLam 12 months ago - 3 comments

#100 - fixes #96 is compressed and compression type fixes

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

#99 - fixes #96 improve export

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

#97 - concat, gzip, bgzip, python 3.10

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

#96 - Improve concat/compression/decompression

Issue - State: closed - Opened by antonylebechec over 1 year ago - 1 comment
Labels: enhancement

#95 - Python 3.10

Issue - State: closed - Opened by antonylebechec over 1 year ago - 1 comment
Labels: enhancement

#94 - #10 improve calculation, add config file

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

#92 - Database dbnsfp

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

#91 - fixes #3 dbNSFP VCF generation, docker .env

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

#90 - fixes #3 dbNSFP, #85 add VCF generation

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

#89 - fix #87, .env

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

#88 - Database dbnsfp

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

#87 - Auto detect threads with CPU available

Issue - State: closed - Opened by antonylebechec over 1 year ago - 1 comment
Labels: enhancement

#86 - Error loading VCF

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

#85 - Out of Memory Error

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

#84 - Issue while using relative input path

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

#83 - fixes calculation, annotation, tests

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

#82 - fix #31 add parquet partition format, import export annotation

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

#81 - fix #9 improve regions database annotation

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

#80 - Add regions annotation parquet

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

#79 - fix #78 logger #4 docs

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

#78 - fix log and verbosity

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

#77 - fix tests

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

#76 - Database assembly structure

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

#75 - Databases Annotations structure

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

#74 - fix #49 fix format refSeq to BED

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

#73 - fix #49 fix tests

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

#72 - Annovar databases with assembly subfolder

Issue - State: closed - Opened by antonylebechec over 1 year ago - 1 comment
Labels: enhancement

#71 - fix #49 add refseq databases

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

#70 - HGVS annotation #49 tests, add version

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

#69 - add hgvs #49

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

#68 - network configuration #67

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

#67 - Network configuration

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