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Sorting GTF file… doesn't sort it #57

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
For which program(s) you want a new feature?
Simulator

Which build of the program(s)?
1.0-RC1

What operating system you use?
unix64

What steps will reproduce the problem?
1. I used the same GTF file as in issue #56 
https://code.google.com/p/fluxcapacitor/issues/detail?id=56
This file is not sorted and has to be sorted by Flux.
Flux sorts it (or says so), then it uses the sorted file and complains because 
the GTF sorted file is not… sorted!

In attachment:
 * flux.log: FluxSimulator output (launched with flux -t simulator --log DEBUG -p GRCh37/sim.200bp.pe.1.0.par --threads 1)
 * mutations.gtf.bz2: the compressed GTF file sorted by FluxSimulator

Original issue reported on code.google.com by mikael.s...@gmail.com on 5 Jul 2011 at 7:21

Attachments:

GoogleCodeExporter commented 8 years ago 
Similar problem.
Simulator 1.0-RC1 x86_64

Simulator crashes with GTF file that worked on previous versions, if I use 
sorted GTF (sorted by older version) it works OK.

Original comment by peter.gl...@gmail.com on 5 Jul 2011 at 7:52

Attachments:

GoogleCodeExporter commented 8 years ago

Original comment by thasso.g...@gmail.com on 6 Jul 2011 at 10:32

GoogleCodeExporter commented 8 years ago 
There was an issue in the sorter (numbers were not treated as numbers due to a 
bug in the cloning code of a line comparator). 

The issue is fixed and incorporated in RC2 which I just uploaded. Please get 
the new version and verify that sorting works now. I tested it with my GTF 
files and the ones appended here and had no problems.

Also note that you can use 'flux -t sortGtf -i <your.gtf> -o <sorted.gtf>' to 
sort a GTF without starting the pipeline.

General note about the sort order. We sort using the following fields in the 
following order:

0 chromosome
6 strand
cluster start - this is the minimal transcript start for a set of overlapping 
genes
transcript start
transcript ID

Original comment by thasso.g...@gmail.com on 6 Jul 2011 at 6:07