Support reference panels in msav format and decay parameter (#128)
* Add new minimac4 binary and adapt execution command
* Add msav reference panels
* Adapt test data to include GT tag
* Fix input data
* Fix input data for hg38 test cases
* Ignore obsolete --myChromosome option
* Update run-tests.yml
* Update run-tests.yml
* Update to new parameter --sites for writing info files
* Add new minR2 parameter to minimac4 and remove R2 pipeline filter
* Add prefix mis_ to all MIS tags in VCF file
* Fix VCF header test case with new prefix
* Update to latest minimac4 binary
* Add min-r2 parameter to command only if minR2 > 0
* Update to pgs-calc version v0.9.10
* Prepare release v1.7.0-rc1
* Update to latest minimac4 (commit 9c653eb)
* Prepare release 1.7.0-rc2
* Update minimac4 to 8498d
* Add HTS tag to m4 format option
* Update minimac4 and rebuild msav files
* Update DefaultPreferenceStore.java
* Fix line number in new test case (from master) due to new M4
* Update to minimac v4.1.0
* Update to minimac v4.1.4
* Add minimac4 decay option
* Prepare release v1.8.0-beta1
* Update imputation engine log to v4.1.4
* Prepare release v1.8.0-beta2
* Update to minimac v4.1.5
* Prepare release v1.8.0-beta3
* Prepare release v1.8.0-beta4 (#126)
Provenance: from installer script
https://github.com/statgen/Minimac4/releases/tag/v4.1.6
---------
Co-authored-by: Andy Boughton <[email protected]>
