the simulator's gtf parser creates wrong spliceform loci numbers

[GoogleCodeExporter]

For which program(s) you want a new feature?
(Simulator)

Which build of the program(s)?
20090811

What operating system you use?
(unix32)

What steps will reproduce the problem?
1.parsing the attached gtf file with the simulator

What is the expected output? What do you see instead?
expected:
spliceforms: 2
loci: 1

What I see instead:
spliceforms: 3
loci: 3

Original issue reported on code.google.com by mun...@gmail.com on 15 Aug 2009 at 3:43

Attachments:

• out.gtf

[GoogleCodeExporter]

Reproduced.

Original comment by gmicha@gmail.com on 15 Aug 2009 at 5:44

• Changed state: Accepted
• Added labels: Simulator

[GoogleCodeExporter]

Problem: a bug in the routine that checks the file sorting: the transcript_id 
of the
first line was ignored in the check, and a warning for multiple equal transcript
identifiers on the same chromosome has been suppressed in the graphical user
interface. The bug affected all files that were sorted by genomic coordinates, 
but
not by transcript_id.

Solution: I removed the bug with the first line and now files non-adajent lines 
of
equal transcript_id strings on the same chromosome are considered unsorted. Fix
contained since build 20090815.

Alpha-Test: The originally attached file out.gtf now triggers a file sorting. 
The
correctly sorted file then produces the expected output

chrI:176-999W   trans1  NC  458
chrI:176-999W   trans2  NC  102

Simulator build 20090815 available 

http://code.google.com/p/fluxcapacitor/downloads/detail?name=FluxSimulator-20090
815.tar.gz&can=2&q=#makechanges

Issue closed.

Original comment by gmicha@gmail.com on 15 Aug 2009 at 5:57

• Changed state: Fixed