BioLegato - Bugs and Workarounds
July. 18, 2018
1. Circular sequences
Problem: Aside from GenBank format, virtually none of the common file formats has a mechanism to designate whether a DNA/RNA sequence is circular or linear.2. blreads - Java error messages
- Reading files: Read the sequence in using File --> Open, NOT Import Foreign Format.
- Changing topology: Edit --> GetInfo. Set topology to Circular or Linear. Click on "Update".
- Use File --> Export Foreign format to export to a format that explicitly allows for specification of a circular topology. Only GenBank or EMBL formats have the ability to specify topology.
In some cases, when blreads completes a task and refreshes the list of files to reflect files created, a Java error message is printed that begins
BioPCD: Command executed successfully, return status: 0
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 2 >= 0
Extensive testing has determined that this bug can be ignored safely. It should be resolved in a future release.
BUGS, Issues and
Bugzilla is the official site for listing and reporting bugs
Also see the Release
Notes for the current version of BIRCH