molgenis / systemsgenetics

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool
https://github.com/molgenis/systemsgenetics/wiki
GNU General Public License v3.0
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Bug fixes and minor improvements to Genotype-IO and GH #643

Closed CAWarmerdam closed 1 year ago

CAWarmerdam commented 1 year ago

Removed unnecessary print statement from bgen writer. Improved handling of preferred genotype format fields for reading VCF files; now it's behaviour of choosing phased/unphased is more like expected (see wiki for details; will update the wiki soon)