molgenis/data-transform-vkgl issues and pull requests

#69 - Use `GCA_000001405.15_GRCh38_no_alt_analysis_set` as `GRCh38` reference

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

#68 - feat: improve run.sh to make it work better

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

#67 - fix: update to make it work

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

#66 - chore(deps): bump guava from 30.0-jre to 32.0.0-jre

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

#65 - Variants deleted in clinvar and later updated again, should be "update" rather than "novel"

Issue - State: closed - Opened by marikaris about 3 years ago
Labels: bug

#64 - Pseudogenes should not be submitted as such to ClinVar

Issue - State: closed - Opened by marikaris about 3 years ago
Labels: bug

#63 - Last lab to be transformed by `run.sh` output gets cut off

Issue - State: open - Opened by marikaris about 3 years ago
Labels: bug

#62 - Use ftp server for data delivery

Pull Request - State: closed - Opened by bartcharbon about 3 years ago - 2 comments

#61 - Fix #60 Valid withdrawn genes using alias or previous symbols

Pull Request - State: closed - Opened by dennishendriksen about 3 years ago - 2 comments

#60 - Valid withdrawn genes using alias or previous symbols

Issue - State: closed - Opened by dennishendriksen about 3 years ago
Labels: bug

#59 - docs: add release info

Pull Request - State: closed - Opened by marikaris over 3 years ago - 2 comments

#58 - Add liftover script for consensus files

Pull Request - State: closed - Opened by bartcharbon over 3 years ago - 2 comments

#57 - Test checklist

Pull Request - State: closed - Opened by bartcharbon over 3 years ago

#56 - Create pull_request_template.md

Pull Request - State: closed - Opened by marikaris over 3 years ago

#55 - Integration tests broken

Issue - State: closed - Opened by marikaris over 3 years ago
Labels: bug

#54 - fix: set null string for csv

Pull Request - State: open - Opened by marikaris over 3 years ago - 2 comments

#53 - introduce vkgl_consensus_add_gene_id.sh

Pull Request - State: closed - Opened by dennishendriksen over 3 years ago - 2 comments

#52 - Treat gene symbols with incorrect casing as invalid

Issue - State: open - Opened by dennishendriksen over 3 years ago
Labels: bug

#51 - chore: remove termcolor

Pull Request - State: closed - Opened by marikaris over 3 years ago - 2 comments

#50 - feat: add script that prepares the output of run.sh for molgenis-py-consensus

Pull Request - State: open - Opened by marikaris over 3 years ago - 2 comments

#49 - Genes with invalid HGNC symbols are always written to errorfile

Issue - State: open - Opened by marikaris over 3 years ago
Labels: bug

#48 - Variant identifiers change when gene symbols change

Issue - State: open - Opened by dennishendriksen over 3 years ago
Labels: bug

#47 - fix: fix grep for done log with >9 logs

Pull Request - State: closed - Opened by marikaris over 3 years ago - 2 comments

#46 - fix(data-release-pipeline): change the done check in run.sh

Pull Request - State: closed - Opened by marikaris over 3 years ago - 2 comments

#45 - feat(release script): add vkgl release script and validation script

Pull Request - State: closed - Opened by marikaris over 3 years ago - 2 comments

#44 - Fix #35: Potential fix

Pull Request - State: closed - Opened by bartcharbon over 3 years ago - 2 comments

#43 - Fix: Missing variants when processing multiple labs at once

Pull Request - State: closed - Opened by dennishendriksen over 3 years ago - 2 comments

#42 - Pipeline outputs "" for empty timestamp input

Issue - State: open - Opened by dennishendriksen over 3 years ago
Labels: bug

#41 - Revert "Consensus generator command-line app"

Pull Request - State: closed - Opened by dennishendriksen over 3 years ago

#40 - Consensus generator command-line app

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

#39 - Variant validator has issues with delins that's possibly an inversion

Issue - State: open - Opened by marikaris over 3 years ago
Labels: bug

#38 - When several cdna/transcripts are specified, the cdna in the LUMC route gets messed up

Issue - State: open - Opened by marikaris almost 4 years ago - 2 comments
Labels: bug

#37 - chore(deps): bump commons-io from 2.6 to 2.7

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 2 comments
Labels: dependencies

#36 - Variants that are reported twice, once with the correct gene and once with an outdated one, are not reported as duplicate

Issue - State: closed - Opened by marikaris almost 4 years ago

#35 - When internet connection is lost and batch of variants is not returned from variant validator, no error is presented

Issue - State: closed - Opened by marikaris almost 4 years ago - 2 comments
Labels: bug

#34 - fix(pom.xml): set java and maven compiler plugin version

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

#33 - fix(pom.xml): set version of maven-compiler-plugin

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

#32 - feat: add gene validation service

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

#31 - Fix: variants mapped incorrectly when anchor is right from variant and anchor is equal to nucleotide change

Pull Request - State: closed - Opened by marikaris about 4 years ago - 2 comments

#30 - Fix/14 incorrect variants

Pull Request - State: closed - Opened by marikaris about 4 years ago - 2 comments

#29 - Bump Guava 20.0 to 30.0-jre (fix CVE-2018-10237 alert)

Pull Request - State: closed - Opened by dennishendriksen about 4 years ago - 2 comments

#28 - Variant formatter reports 'Failed to fetch from SeqRepo' errors

Issue - State: open - Opened by dennishendriksen about 4 years ago
Labels: bug

#27 - Build stability warnings

Issue - State: closed - Opened by dennishendriksen over 4 years ago
Labels: bug

#26 - Variant formatter uses transcript db older than db used by labs

Issue - State: open - Opened by dennishendriksen over 4 years ago
Labels: bug

#25 - Variant formatter uses GRCh37 instead of GRCh37.p13

Issue - State: open - Opened by dennishendriksen over 4 years ago - 1 comment
Labels: bug

#24 - Fix/20 21 code dup doc

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

#23 - Fix/14 incorrect variants

Pull Request - State: closed - Opened by marikaris over 4 years ago - 3 comments

#22 - Variants are rejected with "skipping variant due to error 'x': not a variant: x"

Issue - State: open - Opened by bartcharbon over 4 years ago
Labels: bug

#21 - Missing documentation for hgvs translator flags

Issue - State: closed - Opened by dennishendriksen over 4 years ago
Labels: documentation

#21 - Missing documentation for hgvs translator flags

Issue - State: closed - Opened by dennishendriksen over 4 years ago
Labels: documentation

#20 - hgvs translator code duplication

Issue - State: closed - Opened by dennishendriksen over 4 years ago
Labels: bug

#19 - Translation fails because extrinsic validation is not possible

Issue - State: open - Opened by dennishendriksen over 4 years ago - 1 comment
Labels: bug

#18 - Translator service produces invalid alt values

Issue - State: open - Opened by dennishendriksen over 4 years ago
Labels: bug

#17 - SyntaxError: invalid syntax when starting translator service

Issue - State: open - Opened by dennishendriksen over 4 years ago
Labels: bug

#16 - Content-Type header missing in translator service response

Issue - State: open - Opened by dennishendriksen over 4 years ago
Labels: bug

#15 - Fix/14 incorrect variants

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

#14 - Large number of variants are incorrectly mapped

Issue - State: closed - Opened by marikaris over 4 years ago - 1 comment
Labels: bug

#13 - fix(vkgltablemapper): check if anchor can be removed

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

#12 - Indels are incorrectly normalized

Issue - State: closed - Opened by marikaris over 4 years ago
Labels: bug, being worked on

#11 - fix(validator/mapper): Fix MT chromosome

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

#10 - Variants on MT chromosome are not validated or normalised

Issue - State: open - Opened by marikaris over 5 years ago
Labels: bug

#9 - Final fixes

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

#8 - Id's are too long

Issue - State: closed - Opened by marikaris over 5 years ago
Labels: bug, being worked on

#7 - Vus classifications are mapped to "v" rather than "vus"

Issue - State: closed - Opened by marikaris over 5 years ago
Labels: bug, being worked on

#6 - Lab upload date is not set for alissa

Issue - State: closed - Opened by marikaris over 5 years ago
Labels: bug, being worked on

#5 - Effect with NULL in alissa mapper is not set empty

Issue - State: closed - Opened by marikaris over 5 years ago
Labels: bug, being worked on

#4 - Variant positions are off by one

Issue - State: closed - Opened by marikaris over 5 years ago
Labels: bug, being worked on

#3 - Feat/map data to VKGL model + check for uniqueness

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

#2 - Run tests with maven

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

#1 - Feat/parallel: Improve pipeline

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

GitHub / molgenis/data-transform-vkgl issues and pull requests