layout annotation error?

kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics

BSD 3-Clause "New" or "Revised" License

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layout annotation error? #50

Closed kfuku52 closed 3 years ago

kfuku52 commented 3 years ago

SRR9020424 is annotated as a paired-end sequencing, but its fastq-dump output looks like those generated from single-end SRA. Such SRA will be detected/treated as single-end with a warning. I'm working on it.

kfuku52 commented 3 years ago

fixed in https://github.com/kfuku52/amalgkit/commit/bb88907a5f767191b2b4bf6a11a598e8f1960dba

kfuku52 commented 3 years ago

getfastq could not detect the safely_removed flag correctly when the layout annotation is mismatched. This has been fixed in https://github.com/kfuku52/amalgkit/commit/240948ffc6312a644de6668f7111a66e667c6cc1