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PGEN backend: plink2 conversion canonicalizes unphased allele order and promotes haploid GTs

Status: Open.

#203 In mcvickerlab/GenVarLoader;

· d-laub opened on Jun 1, 2026

with_seqs("variants") (RaggedVariants) does not clip variants to the region window

Status: Open.

#202 In mcvickerlab/GenVarLoader;

· d-laub opened on Jun 1, 2026

gvl.write crashes on all-REF / zero-variant input instead of handling it cleanly

Status: Open.

#201 In mcvickerlab/GenVarLoader;

· d-laub opened on Jun 1, 2026

gvl.write does not validate left-alignment of variants

Status: Open.

#200 In mcvickerlab/GenVarLoader;

· d-laub opened on Jun 1, 2026

gvl.write does not validate variant atomization

Status: Open.

#199 In mcvickerlab/GenVarLoader;

· d-laub opened on Jun 1, 2026

gvl.write exceeds max_mem by >2x on chrom-scale builds (peak >64 GiB with max_mem="32g")

Status: Open.

#162 In mcvickerlab/GenVarLoader;

· bschilder opened on May 18, 2026

Support inserting site-only indels

Status: Open.

#80 In mcvickerlab/GenVarLoader;

· d-laub opened on May 16, 2025

Splicing tests

Status: Open.

#57 In mcvickerlab/GenVarLoader;

· bschilder opened on Apr 15, 2025

support different lengths for each type of sequence

type: enhancementNew feature or requestNew feature or request

Status: Open.

#19 In mcvickerlab/GenVarLoader;

· d-laub opened on Sep 14, 2024