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
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
at java.util.Vector.elementAt(
at javax.swing.table.DefaultTableModel.getValueAt(
at javax.swing.JTable.getValueAt(

Extensive testing has determined that this bug can be ignored safely. It should be resolved in a future release.

BUGS, Issues and Improvements

The BIRCH Bugzilla is the official site for listing and reporting bugs .

Also see the Release Notes for the current version of BIRCH

You can see fixes and improvements planned for upcomming BIRCH releases on the BIRCH ToDo List.

If you really want to see the details of the BIRCH development process, that can be found on the BIRCH Wiki.