No quality output (FASTQ file)

[GoogleCodeExporter]

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

Which build of the program(s)?
20101210

What operating system you use?
unix64

What steps will reproduce the problem?
Set FASTQ to YES in the .par file. 

What is the expected output? What do you see instead?
Instead of a FASTQ file with quality information, a FASTA file is produced 
(without quality information)

Feel free to provide any additional information below.
I never really paid attention to that but I never had a FASTQ output with Flux 
Simulator although FASTQ was always set to YES in the PAR file.
Can Flux Simulator produce quality information in its output?

Original issue reported on code.google.com by mikael.s...@gmail.com on 16 Feb 2011 at 5:18

[GoogleCodeExporter]

Hi, I have a similar problem at the last step but I even did not get a FASTA 
file. Have you solved the problem? Thanks.

Original comment by zhaoha...@gmail.com on 23 Mar 2011 at 8:28

[GoogleCodeExporter]

Original comment by thasso.g...@gmail.com on 1 Apr 2011 at 5:24

• Added labels: Simulator

[GoogleCodeExporter]

Issue 49 has been merged into this issue.

Original comment by thasso.g...@gmail.com on 4 Apr 2011 at 9:45

[GoogleCodeExporter]

Fixed the ArrayOutOfBounds exception. This will be incorporated in the next 
release.

Original comment by thasso.g...@gmail.com on 4 Apr 2011 at 9:46

• Changed state: Fixed

[GoogleCodeExporter]

Issue 50 has been merged into this issue.

Original comment by thasso.g...@gmail.com on 4 Apr 2011 at 9:47

[GoogleCodeExporter]

I may be wrong but that does not look like Issue 50. I mean the whole 
sequencing works fine, I have no error. Two files are created a BED file and a 
FASTA file, with the right number of lines. But since FASTQ is set to YES I 
would expect a FASTQ file with quality information for each read.

Original comment by mikael.s...@gmail.com on 4 Apr 2011 at 9:52

[GoogleCodeExporter]

Right, my mistake, I will look into this.

Original comment by thasso.g...@gmail.com on 4 Apr 2011 at 10:18

• Changed state: Reopened

[GoogleCodeExporter]

We uploaded a largely redesigned simulator version (1.0 RC1) with additional 
logging depth is provided by the --log DEBUG parameter, please post a 
corresponding stderr output if the problem persists for you. 

Issue remains open until confirmed to have disappeared in v1.0 RC1.

Original comment by gmicha@gmail.com on 17 Jun 2011 at 1:36

[GoogleCodeExporter]

RC3 fixes this and incorporates a new error model as well as a way to create 
error models

Original comment by thasso.g...@gmail.com on 26 Jul 2011 at 1:25

• Changed state: Fixed