Update to Savvy 2.0 - Githubissues

jonathonl commented 3 years ago

There is a new version of the SAV file format and this update to the Savvy library adds support for the new file format while maintaining support for SAV v1, BCF, and VCF.

Notes about the upgrade:

SAV 2.0 is an extension of BCF, so it supports all BCF data types (including DS). This means that SAV files can be generated from imputed datasets that have DS but not HDS.
Indices for SAV 2.0 are appended to SAV files instead of being stored as separate S1R files. The option parsing in SAIGE_SPATest.R has been updated to remove the need for specifying --vcfFileIndex and --savFileIndex.
Both htslib and liblzma dependencies have been removed.
Savvy 2.0 drops support for TBI index files in favor of the more modern CSI index for BCF and VCF. Test files in extdata/input/ have been updated accordingly with bcftools index <input_file>.

matuskosut commented 3 years ago

Hi @jonathonl, could you also create official release for new savvy such that it can be properly released on conda and used here as a dependency for Saige package? Currently the only official release I see is 1.3.0: https://github.com/statgen/savvy/releases

jonathonl commented 3 years ago

Yeah, there are still a few things I'd like to tidy up before making a release. I expect it to happen in the next few days. I'll let you know when it's done.

jonathonl commented 3 years ago

Savvy v2.0.0 is now released.

weizhouUMICH / SAIGE

Update to Savvy 2.0 #305