Expose hFILE_backend and hfile_init to allow custom hFILE implementations

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#849 opened on Apr 4, 2019 1 comment 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty: 4/5
Estimated time: 3-5 days
Newbie friendliness: 35/100

Issue type: Feature
Clarity: Mostly clear
Activity status: Stale
Tech stack: c
Domain: backend-api-design

Research direction

Start by reviewing hfile_internal.h, the custom implementation in vg's hfile_cppstream.cpp, the htslib-plugins workaround, and the discussion in #647. Trace how hFILE_backend and hfile_init are currently used and how headers are installed. Done means the supported public interface for custom hFILE implementations is defined and its compatibility expectations are clear.

Written by the indexing model from the issue text.

Description

I have a custom hFILE backend over C++ streams that I have written for vg: https://github.com/vgteam/vg/blob/39ac300bb735abf8350e3d2a7ec0356a0742fd56/src/stream/hfile_cppstream.cpp

It has built just fine up until now, since vg ships htslib as a submodule and I can just include hfile_internal.h from it and get the definitions of hFILE_backend and hfile_init.

But now I want to refactor vg's IO logic into its own project, with a dependency on whatever htslib the environment provides. The htslib install process does not install hfile_internal.h, so I can't get at the definitions I need.

I see now that my work is somewhat redundant with #647, but it seemed like in that thread people thought the right thing to do was to just make the backend system available to client code instead of adding a new callback system over it.

For now I'm going to adopt the workaround from https://github.com/samtools/htslib-plugins and just ship my own version of the header and hope that hFILE_backend never changes. But really the type should be exposed so that custom htslib-version-independent hFILE implementations are possible.

Dominant language: C
Stars: 950
Forks: 475
Avg merge: 3d 13h
Merged PRs (30d): 11

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