Capsid

Web Application

**FIXES**

* Error on JBrowse page

Web Application

**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

Pipeline

**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

Web Application

**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

Pipeline

**FEATURES**

* Adds support for pair-end reads

28 Oct 2011

Fixes
* Fixes JBrowse caching old tracks

20 Oct 2011

Fixes
* Added support for MongoDB authentication

19 Oct 2011

* Initial Release