Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

VCF Download : column changes for standard format #410

Open
Don-Isdale opened this issue Sep 17, 2024 · 1 comment
Open

VCF Download : column changes for standard format #410

Don-Isdale opened this issue Sep 17, 2024 · 1 comment
Assignees
@Don-Isdale

Comments

@Don-Isdale
Copy link
Collaborator

Introduction

The Genotype Table enables the user to download a VCF file containing the last-received VCF genotype lookup result from the server.

Testing the downloaded VCF against the standard

Applying vcf-validator to the downloaded VCF shows some differences from the standard, for example swap the order of the POS and ID columns, add columns QUAL, FILTER, INFO.
@Don-Isdale Don-Isdale self-assigned this Sep 17, 2024
@Don-Isdale
Copy link
Collaborator Author

Don-Isdale commented Feb 3, 2025 •
edited
Loading

Upgrade file download

Issue #370 tracked the upgrade of the frontend framework and libraries.
The library used for file download is not supported in the newer framework version, so
'VCF Download' button has been disabled since that upgrade.

To re-enable 'VCF Download' it will be changed to use the same library function which is now used in :

  • table-brushed 'Download CSV file'
  • datasets-csv 'Datasets Report'

Changes Implemented

352f3b3 feature/vcfDownload Re-enable VCF Download by changing from file-anchor to fileDownloadBlob and fileDownloadAsCSV

Tested OK on local

Successful download of both .vcf.gz and .vcf.txt was completed.

Image

Don-Isdale added a commit that referenced this issue Feb 3, 2025
@Don-Isdale
Re-enable VCF Download by changing from file-anchor to fileDownloadBl…
7356839 
…ob and fileDownloadAsCSV

part of #410 (2nd comment).
manage-genotype.hbs :
 change button ember-csv@file-anchor .vcfExportText to action .vcfExportTextToFile, because file-anchor is not supported in the version of Ember.js framework which #370 upgraded to.
 add input checkbox @userSettings.compressVCF, with label .vcf.gz.

manage-genotype.js : add @userSettings.compressVCF, vcfExportTextToFile().
file-download.js :
 factor fileDownloadBlob() out of fileDownloadAsCSV(); add type as an optional parameter.
 add text2Gzip().
Don-Isdale added a commit that referenced this issue Feb 3, 2025
@Don-Isdale
Re-enable VCF Download by changing from file-anchor to fileDownloadBl…
352f3b3 
…ob and fileDownloadAsCSV

part of #410 (2nd comment).
manage-genotype.hbs :
 change button ember-csv@file-anchor .vcfExportText to action .vcfExportTextToFile, because file-anchor is not supported in the version of Ember.js framework which #370 upgraded to.
 add input checkbox @userSettings.compressVCF, with label .vcf.gz.

manage-genotype.js : add @userSettings.compressVCF, vcfExportTextToFile().
file-download.js :
 factor fileDownloadBlob() out of fileDownloadAsCSV(); add type as an optional parameter.
 add text2Gzip().
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@Don-Isdale Don-Isdale

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@Don-Isdale