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Unsupported sam headers get silently stripped #3251

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2 tasks done
notestaff opened this issue Mar 5, 2024 · 2 comments
Open
2 tasks done

Unsupported sam headers get silently stripped #3251

notestaff opened this issue Mar 5, 2024 · 2 comments
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bug faulty or wrong behaviour of code

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@notestaff
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Does this problem persist on the current main?

  • I have verified the issue on the current main

Is there an existing issue for this?

  • I have searched the existing issues

Current Behavior

Currently, unknown tags in SAM headers are getting silently stripped from files.

Expected Behavior

Given that the SAM format permits user-defined tags, it would be better to pass them unchanged from input to output.

Steps To Reproduce

Try with the pb: tag mentioned in #3215

Environment

SeqAn version: 3.3.0
Operating system: Linux bpb23-acc 5.4.0-136-generic #153-Ubuntu SMP Thu Nov 24 15:56:58 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
Compiler: x86_64-conda-linux-gnu-c++ (conda-forge gcc 12.3.0-2) 12.3.0

Anything else?

No response

@notestaff notestaff added the bug faulty or wrong behaviour of code label Mar 5, 2024
@notestaff
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@eseiler

@notestaff
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P.S. Is there any workaround in the current seqan3 release, that would allow preserving pb: header tags? We're writing a tool that adds tags to bam records, and it should make no other change to the bam file, but right now it also ends up stripping pb: header tags. Thanks for help!
@eseiler

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