FEATURES
- Tab for Project level statistics to the genome page
- Total number of samples displayed in the project list view
- Cancel Edit link to return to main view without saving
- More descriptive page titles
- Pagination added to tables
- Default Mapped tab changed to Alignment
FIXES
- Remove broken Add Sample button on Sample list page
- Broken Edit Alignment button
- Genomes features not displaying even when features existed
- Formatting for Add User popup
FIXES
- Mapped alignemnt positions line up properly with genome positions
- Open new tab when clicking on read in JBrowse
- Adds link to show all samples from genome details page
- Edit User button properly labelled and working
- Added cancer type to sample page
- Users and UserRoles save properly
FIXES
- Subtraction filters unmapped reads before building mapped alignments
FIXES
- Show reads that map to both reference sets in red
FIXES
- Updated README.md
- Corrected JavaScript issues which broke adding users
FIXES
- Corrected Config Access issues
FEATURES
- Config file location can be specified through Java System Property
FIXES
- Deploying under Tomcat or Jetty works again
- OpenJDK compatible (no longer requires Oracle VM)
- 404 issue for reads that didn't map to any gene
FIXES
- Error on JBrowse page
FEATURES
- Simplified installation
- Added embedded Jetty server
- Mapped read details page
- Display read alignment against genome sequence
FIXES
- UserRoles not being deleted with User
- Edit button works in FF 3.6
- Statistics tables sorted by max coverage
FEATURES
- Utility to create FastQ files from unmapped reads
- Utility to return intersection of FastQ files
- Utility to return filter FastQ files
- Added mapq threshold flag to subtraction
- Gbloader can now load bacteria and fungal genomes
- Saves genome sequences to database using GridFS
FIXES
- Reduced memory footprint when calculating statistics
- use subprocesses instead of os.system
- mapq scores filter needs to include 0 <= mapq <=3 due to multiple mapping reads
FEATURES
- New Admin Interface
- Role have access levels for more control over user access
- LDAP option when creating a new user to stop credentials from being sent to keep login control with the LDAP server
- Project owners can control the visibility of their project and user access levels
- Create Alignments from Project page
- Project/Samples/Alignemnts and Users can all be edited and delete
- Reads that map to both pathogen and reference genomes are highlighted
FIXES
- Popups populated through ajax calls
- Grids refreshed rather than forcing page reload
- Moved Admin link to nav bar
FEATURES
- Adds support for pair-end reads
- Fixes JBrowse caching old tracks
- Projects seen in JBrowse filtered by access privileges
- Added support for MongoDB authentication
- Initial Release
- Initial Release