Alpha 6.9: phased-r2 edge case fix

This fixes a numerical edge case that was generating nonsense (not in [0, 1]) phased-r2 results.

Alpha 5.23: --ld edge case fix

This fixes a numerical edge case that was generating nonsense (not in [0, 1]) phased-r2 results.

Alpha 6.8: fix potential --glm linear regression crash

This fixes an uninitialized-variable bug that does not appear to have had any consequences in previous precompiled binaries, but does cause --glm linear regression to crash on Ubuntu 24.04 ARM. This also fixes Linux ARM build breaks in a6.6-a6.7.

Alpha 6.7: fix linear regression crash on extreme missingness

This fixes a segfault or assertion failure that could occur when --glm's linear regression was run with no covariates on data with extremely high missingness.

Alpha 6.6: --r[2]-[un]phased + "--allow-extra-chr 0"

This fixes a bug that occurred when --r[2]-[un]phased and "--allow-extra-chr 0" were used together.

This snapshot of the repo also includes a new vcf_subset utility for rapidly extracting a few columns from a very wide (possibly compressed) VCF, since plink2 --vcf is not designed for that use case.

Alpha 6.5: --check-sex/--impute-sex and FIRTH_CONVERGE_FAIL bugfixes

This fixes a --check-sex/--impute-sex bug that could result in a spurious ".pgen file read failure" error, and an uninitialized-value-multiplied-by-zero bug that could cause unintended FIRTH_CONVERGE_FAIL errors when the uninitialized value was nan.

Alpha 5.22: fix FIRTH_CONVERGE_FAIL bug

This fixes an uninitialized-value-multiplied-by-zero bug that could cause unintended FIRTH_CONVERGE_FAIL errors when the uninitialized value was nan.

Alpha 6.4: Unbreak --import-dosage + --map

This fixes an --import-dosage + --map command-line parsing bug introduced in August.

Alpha 5.21: Unbreak --import-dosage + --map

This fixes an --import-dosage + --map command-line parsing bug introduced in a5.13.

Alpha 6.3: --sort-vars forced-QUAL/FILTER bugfix

This release fixes a segfault that occurred when --sort-vars was specified, .pvar output was requested with a required QUAL/FILTER column, and that column was not present in the input.