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Merged
trishorts merged 6 commits into from
Jul 14, 2026
Merged

Bruker .baf nuget support and bug fix #1096

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62d74a9
Fix IndexOutOfRangeException on profile Bruker data with MS/MS trimming
Alexander-Sol Jul 11, 2026
860dc02
Ship Bruker baf2sql native deps in mzLib NuGet lib root
Alexander-Sol Jul 11, 2026
58f7ace
Merge branch 'master' into BrukerBafNugetSupport
Alexander-Sol Jul 11, 2026
fb1cbde
Fix Bruker .baf reader yielding empty database search results, write…
Alexander-Sol Jul 12, 2026
c92434e
Merge branch 'BrukerBafNugetSupport' of https://github.com/Alexander-…
Alexander-Sol Jul 12, 2026
29d3910
Added additional tests
Alexander-Sol Jul 13, 2026
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289 changes: 237 additions & 52 deletions mzLib/Readers/Bruker/BrukerFileReader.cs
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12 changes: 8 additions & 4 deletions mzLib/Readers/Readers.csproj
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Original file line number Diff line number Diff line change
Expand Up @@ -53,19 +53,23 @@
</ItemGroup>

<ItemGroup>
<None Update="Bruker\baf2sql_c.dll">
<!-- Bruker baf2sql native library + its VC++ 2012 runtime dependencies.
These live in the project root (not a subfolder) so they copy to the output root
and can be resolved by the bare-name DllImport ("baf2sql_c") in BrukerFileReader.
baf2sql_c.dll depends on msvcp110/msvcr110/vcomp110, so all four must sit together. -->
<None Update="baf2sql_c.dll">
<CopyToOutputDirectory>Always</CopyToOutputDirectory>
</None>
<None Update="Bruker\baf2sql_c.lib">
<CopyToOutputDirectory>Always</CopyToOutputDirectory>
</None>
<None Update="Bruker\msvcp110.dll">
<None Update="msvcp110.dll">
<CopyToOutputDirectory>Always</CopyToOutputDirectory>
</None>
<None Update="Bruker\msvcr110.dll">
<None Update="msvcr110.dll">
<CopyToOutputDirectory>Always</CopyToOutputDirectory>
</None>
<None Update="Bruker\vcomp110.dll">
<None Update="vcomp110.dll">
<CopyToOutputDirectory>Always</CopyToOutputDirectory>
</None>
<None Update="Thermo\ThermoFisher.CommonCore.BackgroundSubtraction.dll">
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0 mzLib/Readers/Bruker/baf2sql_c.dll → mzLib/Readers/baf2sql_c.dll
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0 mzLib/Readers/Bruker/msvcp110.dll → mzLib/Readers/msvcp110.dll
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0 mzLib/Readers/Bruker/msvcr110.dll → mzLib/Readers/msvcr110.dll
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0 mzLib/Readers/Bruker/vcomp110.dll → mzLib/Readers/vcomp110.dll
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243 changes: 239 additions & 4 deletions mzLib/Test/FileReadingTests/SpectraFileReading/TestBruker.cs
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12 changes: 8 additions & 4 deletions mzLib/mzLib.nuspec
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Expand Up @@ -83,8 +83,10 @@
<file src="Readers\bin\x64\Release\net8.0\Thermo\ThermoFisher.CommonCore.RawFileReader.dll" target="lib\net8.0" />
<file src="Readers\bin\x64\Release\net8.0\timsdata.dll" target="lib\net8.0" />
<file src="Readers\bin\x64\Release\net8.0\timsdata.lib" target="lib\net8.0" />
<file src="Readers\bin\x64\Release\net8.0\Bruker\msvcp110.dll" target="lib\net8.0" />
<file src="Readers\bin\x64\Release\net8.0\Bruker\msvcr110.dll" target="lib\net8.0" />
<file src="Readers\bin\x64\Release\net8.0\baf2sql_c.dll" target="lib\net8.0" />
<file src="Readers\bin\x64\Release\net8.0\vcomp110.dll" target="lib\net8.0" />
<file src="Readers\bin\x64\Release\net8.0\msvcp110.dll" target="lib\net8.0" />
<file src="Readers\bin\x64\Release\net8.0\msvcr110.dll" target="lib\net8.0" />
<file src="UsefulProteomicsDatabases\bin\x64\Release\net8.0\UsefulProteomicsDatabases.dll" target="lib\net8.0" />
<file src="Transcriptomics\bin\x64\Release\net8.0\Transcriptomics.dll" target="lib\net8.0" />
<!--net8.0-windows target with mzPlot-->
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<file src="Readers\bin\x64\Release\net8.0\Thermo\ThermoFisher.CommonCore.RawFileReader.dll" target="lib\net8.0-windows7.0" />
<file src="Readers\bin\x64\Release\net8.0\timsdata.dll" target="lib\net8.0-windows7.0" />
<file src="Readers\bin\x64\Release\net8.0\timsdata.lib" target="lib\net8.0-windows7.0" />
<file src="Readers\bin\x64\Release\net8.0\Bruker\msvcp110.dll" target="lib\net8.0-windows7.0" />
<file src="Readers\bin\x64\Release\net8.0\Bruker\msvcr110.dll" target="lib\net8.0-windows7.0" />
<file src="Readers\bin\x64\Release\net8.0\baf2sql_c.dll" target="lib\net8.0-windows7.0" />
<file src="Readers\bin\x64\Release\net8.0\vcomp110.dll" target="lib\net8.0-windows7.0" />
<file src="Readers\bin\x64\Release\net8.0\msvcp110.dll" target="lib\net8.0-windows7.0" />
<file src="Readers\bin\x64\Release\net8.0\msvcr110.dll" target="lib\net8.0-windows7.0" />
<file src="UsefulProteomicsDatabases\bin\x64\Release\net8.0\UsefulProteomicsDatabases.dll" target="lib\net8.0-windows7.0" />
<file src="Transcriptomics\bin\x64\Release\net8.0\Transcriptomics.dll" target="lib\net8.0-windows7.0" />
</files>
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