Unsupported sam headers get silently stripped

notestaff commented 4 months ago

Does this problem persist on the current main?

[X] I have verified the issue on the current main

Is there an existing issue for this?

[X] 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 https://github.com/seqan/seqan3/issues/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 commented 4 months ago

@eseiler

notestaff commented 4 months ago

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

seqan / seqan3