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[FEATURE] Allow setting warning stream for sam file #3246

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merged 3 commits into from
Feb 29, 2024

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@eseiler eseiler commented Feb 29, 2024

Resolves #3215

Todo:

  • Documentation
  • Snippet for sam_file_input_options::warning_stream
  • Check whether there are other warnings

@eseiler eseiler force-pushed the feature/sam_warnings branch from c86d6c8 to 62fd6fe Compare February 29, 2024 10:07
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@seqan-actions seqan-actions added lint [INTERNAL] signal for linting and removed lint [INTERNAL] signal for linting labels Feb 29, 2024
@eseiler eseiler force-pushed the feature/sam_warnings branch from dfcf18f to 2f8c3ae Compare February 29, 2024 10:10
@seqan-actions seqan-actions added lint [INTERNAL] signal for linting and removed lint [INTERNAL] signal for linting labels Feb 29, 2024
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codecov bot commented Feb 29, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.18%. Comparing base (c44d090) to head (54532ca).

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #3246   +/-   ##
=======================================
  Coverage   98.17%   98.18%           
=======================================
  Files         269      269           
  Lines       11868    11872    +4     
=======================================
+ Hits        11652    11656    +4     
  Misses        216      216           

☔ View full report in Codecov by Sentry.
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@seqan-actions seqan-actions added lint [INTERNAL] signal for linting and removed lint [INTERNAL] signal for linting labels Feb 29, 2024
@eseiler eseiler force-pushed the feature/sam_warnings branch from eb28180 to 22d8a1a Compare February 29, 2024 13:25
@seqan-actions seqan-actions added the lint [INTERNAL] signal for linting label Feb 29, 2024
@seqan-actions seqan-actions removed the lint [INTERNAL] signal for linting label Feb 29, 2024
@eseiler eseiler force-pushed the feature/sam_warnings branch from 22d8a1a to 54532ca Compare February 29, 2024 13:26
@seqan-actions seqan-actions added the lint [INTERNAL] signal for linting label Feb 29, 2024
@eseiler eseiler marked this pull request as ready for review February 29, 2024 13:27
@seqan-actions seqan-actions removed the lint [INTERNAL] signal for linting label Feb 29, 2024
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@SGSSGene SGSSGene left a comment

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Cool!

@eseiler eseiler merged commit 3fbe403 into seqan:main Feb 29, 2024
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@eseiler eseiler deleted the feature/sam_warnings branch February 29, 2024 13:48
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Successfully merging this pull request may close these issues.

Unsupported SAM header tag in @HD: pb
3 participants