Update to htslib 1.10.2#184

Merged

johanneskoester merged 81 commits intorust-bio:htslib-1.10.2from

brainstorm:htslib-1.10.2

Mar 17, 2020

Commits on Feb 4, 2020

Going through https://github.com/samtools/htslib/blob/develop/README.large_positions.md to spot 64 bit reference position changes and sam_* function renaming. Only 4 errors left, but need to closel…
brainstorm
committed
Repoint submodule to upstream release tag
brainstorm
committed
brainstorm
committed
Try to amend submodule
brainstorm
committed
Handle submodules manually on TravisCI, since it is failing now: https://travis-ci.org/rust-bio/rust-htslib/builds/645772614
brainstorm
committed
Odd balls that would need review marked with XXX. New htslib seems to require libcurl
brainstorm
committed
Add curl-sys crate for hplugin_curl, aws s3 et al
brainstorm
committed
Add conditional libcurl compilation flags
brainstorm
committed
Be nice with cargo fmt [ci skip]
brainstorm
committed
Try installing libcurl meta-package instead of the openssl dependent one?: https://travis-ci.org/rust-bio/rust-htslib/builds/645790138#L1529
brainstorm
committed
Does not work with libcurl-dev metapackage: https://travis-ci.org/rust-bio/rust-htslib/jobs/645812050#L166, rollback and try with bionic ubuntu distro. It does compile locally on OSX
brainstorm
committed
Add matrix compile support for TravisCI, I would like to know why it compiles fine in OSX and fails on Linux now...
brainstorm
committed
PPA source no longer needed for ubuntu bionic? [ci skip]
brainstorm
committed
Bionic packages htslib with gnutls instead of openssl: https://packages.ubuntu.com/source/disco/htslib ... and it even comes with pre-shipped libcurl4-gnutls-dev, so no need to install it explicitl…
brainstorm
committed
sed is not gsed on OSX... not entirely sure this substitution is 100% needed
brainstorm
committed
Add libssl-dev to the mix for the openssl-sys: https://travis-ci.org/rust-bio/rust-htslib/jobs/645825022#L1000. Testsuite seems to run partially now: https://travis-ci.org/rust-bio/rust-htslib/jobs…
brainstorm
committed
Add build-essential in hopes to fix libcurl issue, incorporate https://github.com/rust-bio/rust-htslib/pull/185, fix one testsuite warning
brainstorm
committed
Add curl on default features for hts-sys
brainstorm
committed

Commits on Feb 5, 2020

Point to the right htslib upstream repo, thanks @dlaehnemann [skip ci]
brainstorm
committed

Commits on Feb 8, 2020

Commits on Feb 9, 2020

tid is i64 now, CRAM vs BAM test l_data is off by 3 and m_data is off too
brainstorm
committed

Commits on Feb 10, 2020

There should be no need for travis_wait with -v
brainstorm
committed

Commits on Feb 20, 2020

Debugging htslib structs with @jkbonfield guidance...
brainstorm
committed

Commits on Feb 21, 2020

Disable osx and musl-cross homebrew on the TravisCI matrix since it times out anyway, start looking into l_extranul and alignment issues for CRAM/BAM. Add curl_sys crate in hts-sys/src/lib.rs.
brainstorm
committed

Commits on Feb 28, 2020

Commits on Mar 1, 2020

Indicate dependencies and build flags required for OSX [ci skip].
brainstorm
committed

Commits on Mar 10, 2020

Commits on Mar 11, 2020