v1.0.1

This release captures several updates and bug fixes to the HapASeg method that followed the writing and analysis of the HapASeg publication (Priebe et al. 2026). To reproduce the manuscript, please use v1.0.

What's Changed

Allow custom covariates to be specified by @julianhess in #11
updating for configuration with hetpulldown EM method by @gpmoorhead1 in #12
adding ref fasta overwrite and fixing snp_list typo by @gpmoorhead1 in #17
Added the most recent version of the paper that I have. by @ormorni in #19
merge master by @dheiman in #20
Added set -eux to some task scripts (so they fail properly) by @dpmerrell in #14
Crash fix and more outputs by @ormorni in #21
Update docker for Hapaseg_collect_coverage_mcmc by @dheiman in #24
Various HapASeg updates by @ormorni in #25
Mutect null bytes by @SamWisedev in #26
Hapaseg local by @oliverpriebe in #28
update license to GPL3 by @oliverpriebe in #30
Update readme and ref_file handling for more accessible installation by @oliverpriebe in #32