FastQ conversion solid quality of "."-> " "

[GoogleCodeExporter]

When reading a solid .qual file, any reads containing no-calls or "." (quality 
score =-1) are given quality codes of space " " by cutadapt.  This interferes 
with downstream programs.

While space is the 'correct' ascii conversion, it seems that quality scores of 
-1 are not supported in fastq.  Converting to 0 (ascii=!) is how other 
conversion programs handle the difficulty.

(original csfasta)
> T222231333010222210330210133311021330211103.1032.211031323112320133330321222
(original qual)
> 17 14 26 23 31 14 26 31 14 14 21 26 28 27 14 31 14 14 26 31 17 14 14 13 14 14 
17 14 21 17 17 14 27 14 14 21 27 21 14 29 14 14 -1 31 14 14 17 -1 27 14 14 27 
14 23 26 14 31 14 21 28 14 14 14 21 21 17 23 14 14 14 14 30 23 17 14 

(cutadapt output) "Actual output"
/;8@/;@//6;=</@//;@2//.//2/622/<//6<6/>// @//2 <//</8;/@/6=///6628////

(galaxy's Convert.py output) "Expected output"
/;8@/;@//6;=</@//;@2//.//2/622/<//6<6/>//!@//2!<//</8;/@/6=///6628////

Original issue reported on code.google.com by jerpars...@gmail.com on 22 Oct 2012 at 7:28

[GoogleCodeExporter]

You can get the behavior you want by using the '-z' command-line option. Which 
programs gave you trouble? Perhaps I should enable the -z option by default.

Original comment by marcel.m...@tu-dortmund.de on 22 Oct 2012 at 10:15

• Added labels: Type-Other
• Removed labels: Type-Defect

[GoogleCodeExporter]

Sorry to have missed that option.  By the time i knew i needed it, i'd 
forgotten that it existed.
Bowtie(0.12.7) was what I was having trouble with.

Original comment by jerpars...@gmail.com on 23 Oct 2012 at 2:20

[GoogleCodeExporter]

Thanks for the reply. I'll update the documentation such that it explicitly 
mentions the -z parameter. Perhaps it also makes sense to enable -z by default.

Original comment by marcel.m...@tu-dortmund.de on 23 Oct 2012 at 3:19

[GoogleCodeExporter]

Original comment by marcel.m...@tu-dortmund.de on 4 Dec 2012 at 9:55

• Changed state: Fixed