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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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racon does not manage fastq files with multiple-line read sequence #67

Closed jeanlain closed 6 years ago

jeanlain commented 6 years ago

When specifying a fastq with line returns within sequences/quality data, racon would tell:

[bioparser::FastqParser] error: invalid file format!

although line returns within read sequences are perfectly valid in fastq, AFAIK.

rvaser commented 6 years ago

Hello, although it is allowed to wrap sequence and quality strings in FASTQ format, it complicates parsing and we decided against it (only 4 lines per read are supported).

Best regards, Robert

rvaser commented 6 years ago

@jeanlain, is the wrapping really necessary? Are any new FASTQ files generated with either NGS or TGS wrapped?

jeanlain commented 6 years ago

Thanks for the reply. seqtk subseq generates wrapped fastq by default

rvaser commented 6 years ago

I'll see if it isn't a big nuisance.

rvaser commented 6 years ago

@jeanlain, the latest commit now supports wrapped FASTQ files. I'll publish a release soon.

rvaser commented 6 years ago

Released in version 1.3.0.

jeanlain commented 6 years ago

Great, thanks