Simulator cannot handle identical transcript IDs

[GoogleCodeExporter]

For which program(s) you want a new feature?
(Capacitor/Simulator/Both/Tetris)
Simulator

Which build of the program(s)?
(look it up in the .prop file in the ./bin folder of the installation)
20100330

What operating system you use?
(unix32, unix64, win32, win64, macPPC32, macX8632, macX8664, other;
see /proc/cpuinfo, Settings->Control Panel->System, Apple->About this Mac)
all

What steps will reproduce the problem?
Input annotation with multiple identical transcript names for different
annotations (i.e., lengths).

What is the expected output? What do you see instead?
There are various effects, one is that abnormally many poly-A reads are
produced, as all reads falling after the shorter transcript length are
interpreted to be inside the poly-A.

Original issue reported on code.google.com by gmicha@gmail.com on 20 Apr 2010 at 4:01

[GoogleCodeExporter]

Anchored transcript IDs on genomic location of their annotation to resolve
conflicting hash values of different annotations.

Original comment by gmicha@gmail.com on 20 Apr 2010 at 4:02

• Changed state: Fixed

[GoogleCodeExporter]

fix in build 20100427

Original comment by gmicha@gmail.com on 26 Apr 2010 at 10:45