More CI checks, clippy, deps updates.

10XGenomics / bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines

MIT License

59 stars 6 forks source link

More CI checks, clippy, deps updates. #29

Closed adam-azarchs closed 3 years ago

adam-azarchs commented 3 years ago

Update dependencies, including some for security advisories.
Set up cargo-deny and clippy checks in CI.
Update rust version to 1.55.
Remove unused dependencies.
Mostly automated fixups for issues detected by clippy.

adam-azarchs commented 3 years ago

mac builder is failing with

/.../hts-sys-d02b8e5dce419f3c/out/htslib/sam.c:2331:21: error: implicit declaration of function 'usleep' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
                    usleep(10000);
                    ^

Not sure if this is due to updating rust-htslib, cc, or just a compiiler update for the mac build image. I don't have a mac to test on, which makes debugging annoying.