Acedb Parsing Bug

Following a report by a user at Sanger we have found a bug has been introduced into the way acedb parses in data, the bug has been in the code for several years so its surprising it has not come to light before.

The problem can be summarised as follows:

if you create an object like this this:


CDS : "R09E10.1"

Sequence : "Eds_sequence"
CDS_child "R09E10.1" 11111 22222


and then wish to change the CDS coords like this:


Sequence : "R09E10"
-D CDS_child "R09E10.1" 11111 22222
CDS_child "R09E10.1" 33333 44444


You end up with "R09E10" looking like this:


Sequence R09E10
  SMap    S_Child     CDS_child   R09E10.1


i.e. you have lost the new coordinates from your change.

There is a work around in that if you change the coords in two stages then all will be fine:

Sequence : "R09E10"
-D CDS_child "R09E10.1" 11111 22222

Sequence : "R09E10"
CDS_child "R09E10.1" 33333 44444

We are working on a fix for this but it has proved more complex than originally thought. Once the code has been fixed we will announce it here. In the meantime if you have any questions about this bug please contact the AceDB developers.