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IGBB / quack

A FASTQ quality assessment tool
GNU General Public License v3.0
14 stars 5 forks source link

Issue when visualizing the output SVG #16

Closed nmendozam closed 4 years ago

nmendozam commented 4 years ago

Hi, I have been trying to use this program, but I have some trouble to find how to visualize the output. I have used the below line, and effectively I get an output :

quack -1 B-LFC1.fq.gz -2 B-LFC2.fq.gz -a Sequencing_adaptors.fasta.gz > B-LFC.svg

But when I try to visualize it i get something like this: A I know is wrong because when I try to open it in Inkscape, I see the following sort of disassembled image: imagen

Or perhaps is it an issue in the input data rather than the output?

maa146 commented 4 years ago

Could you send the svg please? Also, do you know if the phred64 encoding the tool guessed is correct. I believe I've found the issue (a bug in our code), but I want to verify.

The second image is a known issue between the svg renderer used by Inkscape and the transformations used in the image. Unfortunately, there's not a simple fix.

nmendozam commented 4 years ago

Fastqc says the encoding is Illumina 1.5, I don't know if that is what you refer by phred64, if not please tell how to find out the encoding, and I will gladly do it. This is the link to the SVG: https://drive.google.com/file/d/1eyJVhUKD4361PgLpCiGJRGBvBI1to4ag/view?usp=sharing

maa146 commented 4 years ago

Thanks, Illumina 1.5 is phred64.

The new commit should fix this issue; however, we won't be able to update the binaries until next week. I'll leave the issue open until then.

nmendozam commented 4 years ago

I have compiled it, and it works. Thank you.

adamthrash commented 4 years ago

A new release has been created, and the binaries in the repo have been updated.