bioinfo-chru-strasbourg/howard issues and pull requests

#66 - add genomes download #3, fixes and cleaning

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

#65 - fix duckdb extension loading

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

#64 - clean duckdb installation

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

#63 - Refactor with database

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

#62 - User Database to export in Variants

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

#61 - Use Database to annotate with Parquet, VCF...

Issue - State: closed - Opened by antonylebechec over 1 year ago - 2 comments

#60 - remove BCF format as not processing with python

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

#59 - fix #44, #57 export, #58 add conn as database

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

#58 - Add duckDB conn as a database type

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

#57 - Add database export into another format

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

#56 - fix #44 #53 #54 #55

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

#55 - Create header from existing columns in database

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

#54 - Add possibility to force database format

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

#53 - Add sqlite as annotation database format

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

#52 - fix #50 #51 #44

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

#51 - Add header management in Database

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

#50 - Add JSON as a database format

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

#49 - Add HGVS annotation

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

#48 - fix #44 tests

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

#47 - Database object

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

#46 - Bug when annotate with duckdb

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

#45 - Move to java17

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

#44 - Create Database object for annotation database

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

#43 - fix args nargs help #35 doc #4

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

#42 - fix download tool args

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

#41 - some improvements

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

#40 - fix and improve and add multi_variant

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

#39 - fix and improve and add multi_variant

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

#38 - Improve from annovar

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

#37 - improve from_annovar tool #29

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

#36 - verbosity argument failed

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 1 comment
Labels: bug

#35 - Download Annovar DB issue

Issue - State: closed - Opened by JbaptisteLam almost 2 years ago - 4 comments

#34 - Miss fastparquet library

Issue - State: closed - Opened by JbaptisteLam almost 2 years ago - 1 comment

#33 - Validation tool

Issue - State: open - Opened by antonylebechec almost 2 years ago
Labels: enhancement

#32 - Add annotation "parquet" with VCF format files

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 3 comments
Labels: enhancement

#31 - Add parquet partitioned

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 1 comment
Labels: enhancement

#30 - improve perf using parquet #29

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

#29 - Tool from_annovar refactor with duckdb

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 3 comments
Labels: good first issue

#28 - fix from_annovar tool, add test #27

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

#27 - Fix from_annovar tool

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 1 comment
Labels: bug, enhancement

#26 - add output from sqlite connexion format #24

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

#25 - Add JSON input/output/annotations

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

#24 - Improve export output

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 1 comment

#23 - Load input file after check existing mandatory column

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

#22 - refactor load data with read_csv_auto

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

#21 - Annovar to VCF/Parquet #20

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

#20 - Annovar database to VCF/Parquet

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 2 comments
Labels: enhancement

#19 - improve calculations #17, add variant_id #12, improve trio #18

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

#18 - Trio calculation

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 1 comment

#17 - Improve calculation tool

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 1 comment

#16 - Structure python files with tools folder

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 1 comment

#15 - command help with subcommand and arguments groups

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 1 comment
Labels: enhancement

#14 - Check SV annotation (check snpEff)

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 1 comment

#13 - Deal with #CHROM column in db

Issue - State: open - Opened by antonylebechec almost 2 years ago

#12 - Create variant_id on uniq variant

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 1 comment
Labels: enhancement

#11 - Calculation with snpEff

Issue - State: open - Opened by antonylebechec almost 2 years ago
Labels: enhancement

#10 - Classification process

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 1 comment
Labels: enhancement

#9 - Parquet annotation with BED format

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 1 comment
Labels: enhancement

#8 - Multiple VCF as input

Issue - State: open - Opened by antonylebechec almost 2 years ago
Labels: enhancement, wontfix

#7 - Table for samples/genotypes

Issue - State: open - Opened by antonylebechec almost 2 years ago
Labels: enhancement

#6 - Variants deduplication

Issue - State: open - Opened by antonylebechec almost 2 years ago
Labels: enhancement

#5 - SQlite format for main db connexion, input/output and annotation

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 2 comments
Labels: enhancement, help wanted

#4 - Docs

Issue - State: open - Opened by antonylebechec almost 2 years ago

#3 - Add download annotations

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 2 comments
Labels: enhancement

#2 - Add calculation operations

Issue - State: closed - Opened by antonylebechec almost 2 years ago - 1 comment
Labels: enhancement

#1 - Add files via upload

Pull Request - State: closed - Opened by bioinfo-chru-strasbourg about 6 years ago - 1 comment

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