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.

Alpha 5.20: --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.

Alpha 6.2: --set-{all,missing}-var-ids bugfix

--set-all-var-ids and --set-missing-var-ids should now work properly when $a is used in the template string without $r.

Alpha 5.19: --set-{all,missing}-var-ids bugfix

--set-all-var-ids and --set-missing-var-ids should now work properly when $a is used in the template string without $r.

Alpha 6.1: --make-pgen segfault fix

This build fixes a --make-pgen segfault that occurred when filtering samples from multiallelic variants.

Alpha 6.0: --r[2]-[un]phased

New features:

• LD-matrix computation (--r[2]-unphased)
• --glm qt-residualize mode
• --hwe enhancements for biobank-scale data: support for p-values < 2.23e-308, and sample-size-based thresholds
• --ref-allele/--alt1-allele/--ref-from-fa/--maj-ref support for multiallelic variants
• --check-sex/--impute-sex

Other significant behavior changes relative to alpha 5:

• --allow-extra-chr is never necessary any more
• --set-all-var-ids and related flags are now applied to all --pmerge[-list] inputs
• Polyploid genotypes in VCF/BCF files now default to triggering an error; this behavior is controlled by the --polyploid-mode flag
• -log10(x) column names now consistently start with "NEG_LOG10_", instead of "LOG10_"
• --adjust[-file] QQ column is no longer affected by the 'log10' modifier
• Most computations now consider unknown-sex samples on chrY, unless they explicitly state otherwise