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Upstream handlegraph Google-ification behind build flags - #106

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Upstream handlegraph Google-ification behind build flags#106
adamnovak wants to merge 13 commits into
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@adamnovak

@adamnovak adamnovak commented Aug 13, 2026

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This brings in the changes @mobinasri made for pangenome-aware DeepVariant and tries to put particularly Googley ones (like not throwing exceptions) behind build flags.

Much of the work here is synthetic, so I need to review it before anyone else looks at it.

This is related to vgteam/sdsl-lite#21

mobinasri and others added 10 commits September 19, 2024 19:58
Update trivially_serializable.cpp
Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>
Assisted-by: Claude Code:claude-sonnet-5
Add HANDLEGRAPH_USE_EXCEPTIONS (default ON, matches current behavior)
and HANDLEGRAPH_USE_ABSEIL_LOGGING (default OFF) CMake options. With
exceptions off, fatal errors go through ABSL_LOG(FATAL) if Abseil
logging is enabled, or stderr + std::abort() otherwise. Needed to build
libhandlegraph into exceptions-free Bazel binaries such as DeepVariant.

Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>
Assisted-by: Claude Code:claude-sonnet-5
…ucted exception

Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>
Assisted-by: claude-code:claude-sonnet-5
Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>
Assisted-by: claude-code:claude-sonnet-5
Automated Commit and others added 3 commits August 17, 2026 15:05
Assisted-by: Claude:claude-sonnet-5
Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>
…ns directly

Assisted-by: Claude:claude-sonnet-5
Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>
Assisted-by: Claude:claude-sonnet-5
Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>
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3 participants