search

CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets
MIT License
491 stars 190 forks source link

Dedup errors if input BAM file is empty #624

Open IanSudbery opened 10 months ago

TomSmithCGAT commented 8 months ago

For clarity, what should the behaviour be? A more useful error message?

IanSudbery commented 8 months ago

I would say that a warning might be most obvious thing. I can see there might be times when umi_tools is in a pipeline, when it might be useful for it to be able to process empty files, just so as not to disrupt a pipeline where for e.g. one of the samples had all its reads filtered out.

Ian Sudbery (He/Him) Senior Lecturer in Bioinformatics, Sheffield Institute for Nucleic Acids, School of Biosciences, The University of Sheffield.

web: www.sudlab.co.uk Tel: 0114 222 2738 Twitter: IanSudbery Show Calendar Availability https://calendar.google.com/calendar/u/0?cid=aS5zdWRiZXJ5QHNoZWZmaWVsZC5hYy51aw

On Thu, 7 Mar 2024 at 10:53, Tom Smith @.***> wrote:

For clarity, what should the behaviour be? A more useful error message?

— Reply to this email directly, view it on GitHub https://github.com/CGATOxford/UMI-tools/issues/624#issuecomment-1983254131, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABJELDQXFNVDF4J42E66CYTYXBBJPAVCNFSM6AAAAABCITJNECVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBTGI2TIMJTGE . You are receiving this because you authored the thread.Message ID: @.***>