theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
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[SRA-Fetch] Add additional check for SRA-Lite format when reads are marked as "reject" #480

Open cimendes opened 1 month ago

cimendes commented 1 month ago

:bug:

:pencil: Describe the Issue

Reject reads have a set quality encoding of 3, which is represented by the '$' character

https://www.ncbi.nlm.nih.gov/sra/docs/sra-data-formats/