Ecosyste.ms: Issues

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GitHub / bihealth/ngs-chew issues and pull requests

#89 - chore(deps): bump mypy from 1.12.1 to 1.13.0

Pull Request - State: closed - Opened by dependabot[bot] 26 days ago
Labels: dependencies

#88 - chore(deps): bump mypy from 1.12.0 to 1.12.1

Pull Request - State: closed - Opened by dependabot[bot] about 1 month ago
Labels: dependencies

#87 - chore(deps): bump black from 24.8.0 to 24.10.0

Pull Request - State: open - Opened by dependabot[bot] about 1 month ago
Labels: dependencies

#86 - chore(deps): bump mypy from 1.11.2 to 1.12.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 month ago
Labels: dependencies

#85 - chore(deps): bump mypy from 1.11.1 to 1.11.2

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies

#84 - chore(deps): bump mypy from 1.11.0 to 1.11.1

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#83 - chore(deps): bump black from 24.4.2 to 24.8.0

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#82 - chore(deps): bump mypy from 1.10.1 to 1.11.0

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#81 - chore(deps): bump mypy from 1.10.0 to 1.10.1

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#80 - chore(deps): bump mypy from 1.9.0 to 1.10.0

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#79 - chore(deps): bump black from 24.4.0 to 24.4.2

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#78 - chore(deps): bump black from 24.3.0 to 24.4.0

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#77 - Create feature comparison matrix

Issue - State: open - Opened by xiamaz 8 months ago
Labels: documentation

#76 - chore: update gitignore to include direnv file

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

#75 - chore: release 0.9.5

Pull Request - State: open - Opened by varfish-bot 8 months ago - 1 comment
Labels: autorelease: pending

#74 - docs: Add installation requirements for successfully running ngs-chew

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

#73 - chore(deps): bump black from 24.2.0 to 24.3.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies

#72 - chore(deps): bump mypy from 1.8.0 to 1.9.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#71 - chore: release 0.9.4

Pull Request - State: closed - Opened by varfish-bot 9 months ago - 2 comments
Labels: autorelease: tagged

#70 - fix: issue with truthiness of numpy array

Pull Request - State: closed - Opened by holtgrewe 9 months ago - 1 comment

#69 - fix: resolving chrX het/hom issue (#68)

Pull Request - State: closed - Opened by holtgrewe 9 months ago - 1 comment

#68 - Finally fix chrX sites issue

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

#67 - fix: using previous chrX sites to fix sex determination (#64)

Pull Request - State: closed - Opened by holtgrewe 9 months ago - 1 comment

#66 - chore(deps): bump black from 23.12.1 to 24.2.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#65 - chore(deps): bump black from 23.12.1 to 24.1.1

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#64 - The `chrx_het_hom` column has no values

Issue - State: open - Opened by Nicolai-vKuegelgen 10 months ago - 1 comment
Labels: bug

#63 - chore: release 0.9.3

Pull Request - State: closed - Opened by varfish-bot 10 months ago - 3 comments
Labels: autorelease: tagged

#62 - fix: coercing chrX hom/het ratio from None to 0

Pull Request - State: closed - Opened by holtgrewe 10 months ago - 1 comment

#61 - chore: release 0.9.2

Pull Request - State: closed - Opened by varfish-bot 11 months ago - 1 comment
Labels: autorelease: tagged

#60 - fix: release-please action

Pull Request - State: closed - Opened by holtgrewe 11 months ago - 1 comment

#59 - chore: release 0.9.1

Pull Request - State: closed - Opened by varfish-bot 11 months ago - 1 comment
Labels: autorelease: tagged

#58 - fix: remove versioneer (Python 3.12+)

Pull Request - State: closed - Opened by holtgrewe 11 months ago - 1 comment

#57 - fix: Fills the stats line

Pull Request - State: closed - Opened by ericblanc20 11 months ago - 1 comment

#56 - Empty stats output

Issue - State: closed - Opened by ericblanc20 11 months ago
Labels: bug

#55 - feat: tests with larger (excerpt) datasets

Pull Request - State: closed - Opened by holtgrewe 11 months ago - 2 comments

#54 - Migrate from click to typer

Issue - State: open - Opened by holtgrewe 11 months ago
Labels: enhancement

#53 - ci: adding automerge for dependabot

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

#52 - docs: adding badges to README

Pull Request - State: closed - Opened by holtgrewe 11 months ago - 1 comment

#51 - docs: adding sphinx-based documentation

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

#50 - chore(deps): bump mypy from 1.4.1 to 1.8.0

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#49 - chore(deps): bump black from 22.3.0 to 23.12.1

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#48 - chore(deps): update flake8 requirement from <6.0,>=5.0.4 to >=5.0.4,<8.0

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#47 - chore: adding .github/ files for templates and dependabot

Pull Request - State: closed - Opened by holtgrewe 11 months ago - 1 comment

#46 - ci: adding codecov

Pull Request - State: closed - Opened by holtgrewe 11 months ago - 1 comment

#45 - chore: release 0.9.0

Pull Request - State: closed - Opened by varfish-bot 11 months ago - 2 comments
Labels: autorelease: tagged

#44 - ci: use varfish-bot GitHub token in release-please CI

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

#43 - ci: attempt to bump Python versions in CI

Pull Request - State: closed - Opened by holtgrewe 11 months ago - 1 comment

#42 - feat: updating sites files for stable RSIDs

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

#41 - Review sites files

Issue - State: closed - Opened by holtgrewe 11 months ago

#40 - chore: release 0.8.1

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#39 - fix: sites for GRCh38 (#24)

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

#38 - fix: Remove all duplicated regions in bed files

Pull Request - State: closed - Opened by giacuong171 over 1 year ago - 2 comments

#37 - Duplicated regions in bed file

Issue - State: closed - Opened by giacuong171 over 1 year ago - 2 comments

#35 - feat: add "serve" command (#24)

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

#34 - Also run "bcftools polysomy" as we run "bcftools roh"

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

#33 - Compute homozygosity as a further statistics

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

#32 - The serve command should show relatedness

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

#31 - Compute fingerprint from FASTQ

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

#30 - Compute fingerprint from VCF

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

#29 - Compute projection on IGSR populations

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

#28 - Pedigree consistency checks

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

#27 - Improve relatedness plotting performance

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

#26 - chore: release 0.8.0

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#25 - feat: roh calling with "bcftools roh"

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

#24 - Add "server" feature

Issue - State: closed - Opened by holtgrewe almost 2 years ago

#23 - chore: release 0.7.1

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#22 - fix: fixing chrX sites BED files

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

#21 - feat: using coding regions for chrX sites (#20)

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

#20 - Refine the chrX sites BED files

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

#19 - feat: write out ngs-chew version to header

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

#18 - feat: interpret samtools idxstats output

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

#17 - fix: use actual peddy formulat for relatedness

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

#16 - Allow to specify targets BED file for WES data

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

#15 - feat: collect chrX SNP information for sex identification (#12)

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

#14 - chore: release 0.7.0

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#13 - feat: gather samtools idxstats output

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

#12 - Collect alternate allele fraction from gnomAD chrX SNPs with frequency >=5%

Issue - State: closed - Opened by holtgrewe almost 2 years ago - 5 comments

#11 - Also gather samtools idxstats output and store as string

Issue - State: closed - Opened by holtgrewe almost 2 years ago

#10 - chore: switch to click for argument parsing

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

#9 - fix: formula for relatedness was off by *2

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

#8 - chore: release 0.6.0

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#7 - feat: allow writing allele fraction to fingerprint file

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

#6 - The min depth option is broken

Issue - State: open - Opened by holtgrewe almost 2 years ago
Labels: bug

#5 - chore: release 0.5.1

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#4 - fix: fix for the setup.py based build

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

#3 - chore: release 0.5.0

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#2 - feat: adding README file (#1)

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

#1 - Create README file

Issue - State: closed - Opened by holtgrewe almost 2 years ago