kjolley / BIGSdb

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

https://pubmlst.org/software/bigsdb/

kjolley/BIGSdb Issues

Sequence attribute search in curator interface has plugin buttons that lead to wrong analysis
Closed a month ago
Indicate LINcode of closest matching cgST in sequence query
Updated a month ago
Add seqbin_downloads_require_login option
Closed 2 months ago
Add option to hyperlink to different address depending on regex of field value
Closed 2 months ago
Breadcrumb links on permissions page are not complete
Closed 2 months ago1
FastaExport and ProfileExport plugins should respect the values of allele_downloads_require_login and profile_downloads_require_login
Closed 2 months ago
Suggestion on round and lround module of POSIX
Closed 2 months ago1
Check GenomeComparator/SNPsites ref sequence FASTA file
Closed 2 months ago
The isolate select list in Export.pm uses the count of genomes to decide whether to use a scrolling list
Closed 3 months ago1
Add option to export LINcode prefixes of specific length
Updated 3 months ago
Add option to ignore '0' in scheme completion stats
Closed 3 months ago1
Chart of core loci y-axis is mislabelled
Closed 3 months ago
Some genome submissions can be finalized with invalid assembly filenames uploaded
Updated 4 months ago1
Query_interface_fields table does not have id set as foreign key
Closed 4 months ago
Have a way of indicating in isolate info and data export that there are multiple sequence tags for a locus
Closed 4 months ago
Add option to disable downloads in a specific database configuration
Closed 4 months ago1
Make locus extended attributes accessible for export
Updated 4 months ago
Add query items to the isolate database non-dashboard contents page righthand sidebar
Closed 4 months ago
List query box is not populated when used and paging back to first page in a TableQuery
Closed 4 months ago
Database-specific configuration?
Closed 4 months ago2
Option to require login for allele and profile downloads from web interface
Closed 4 months ago
Make private data more obvious in exports
Closed 4 months ago
Allele sequence checkbox occasionally is not automatically checked when an exact match allele is found on web scan
Updated 4 months ago1
Add permissions to enable download of private data belonging to other people
Updated 4 months ago
Add option for scannew to only scan records that have passed assembly checks.
Closed 4 months ago
Add option for scannew.pl to not check private records
Closed 4 months ago
Disable private data inclusion in export by default
Updated 4 months ago
Add option to disable downloads of private data owned by someone else to which access has been shared
Updated 4 months ago
Hyperlink schemes on isolate info page to link to their descriptions
Closed 4 months ago
The checkbox when scanning for missing loci is displaced to the wrong column
Closed 5 months ago
Add option to sequence query page to pull closest cgST and nearest matches using LINcodes
Updated 5 months ago
Add option to schemes table to use cache for maindisplay results
Updated 5 months ago
Labels for year bar chart in dashboard can be too cluttered where multiple years have same value
Closed 5 months ago
Scheme with analysis=false should not be listed on tag scan page.
Closed 5 months ago
Use multiselect box in plugin field inclusion selection
Closed 5 months ago1
Limit extracted sequences width to 100bp to ensure it lines up with translated sequence
Closed 5 months ago
Seqbin breakdown as admin on private records using job manager do not show isolate names
Closed 5 months ago1
Flag dropdown boxes don't appear on tag scan page if there are very few rows and the page doesn't scroll
Closed 6 months ago1
"lround" is not exported by the POSIX module
Closed 6 months ago7
Disabled schemes should not appear in curator interface
Closed 6 months ago
Field breakdown does not display Unicode characters correctly in scheme field dropdown boxes
Closed 6 months ago
Unitialized variable error in logs if no entry for weasyprint in bigsdb.conf when running configuration check
Closed 6 months ago
Existing allele tooltip in tag scan page does not display unicode characters correctly
Closed 6 months ago1
Hyperlink PubMed id on publication query results page
Closed 6 months ago
Make sure query dashboard is generated for Publication breakdown
Closed 6 months ago
Add option to automatically flag 'ambiguous read' sequences that are otherwise CDS
Closed 6 months ago
Add option to select all incomplete alleles for tagging in tag scan interface
Closed 6 months ago
Add option to require users be logged in to run jobs that require the job manager
Closed 6 months ago
Add option to filter composite fields by database view
Updated 6 months ago
template.pm Module Perl Template dependency
Closed 7 months ago2