[med-svn] [Git][med-team/plink2][master] Update upstream changelog

[Dylan Aïssi]

Dylan Aïssi pushed to branch master at Debian Med / plink2


Commits:
cce84c08 by Dylan Aïssi at 2021-02-04T12:12:13+01:00
Update upstream changelog

- - - - -


1 changed file:

- debian/upstream.docs/upstream.changelog


Changes:

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debian/upstream.docs/upstream.changelog
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@@ -1,6 +1,26 @@
 # Copy/Paste from https://www.cog-genomics.org/plink/2.0/
 
-28 Oct 2020: Multipass "--export A" bugfix. If you've previously run plink2 "--export A" on a file too large to fit in memory, we recommend that you rerun with this build.
+3 Feb 2021: Fixed .pvar loading bug that triggered when FILTER values were relevant at the same time as either INFO/PR or CM values. .ped-derived filesets containing variants where both REF and ALT are missing are permitted again (such variants were prohibited in recent builds). --vcf-ref-n-missing flag added to simplify re-import of .ped-derived VCFs. Removed extra tabs from --pgen-diff output.
+
+23 Jan: --chr-set now sets MT to haploid. ##chrSet .pvar header line without the corresponding command-line flag now initializes chrX, chrY, and MT ploidy correctly.
+
+18 Jan: ##chrSet .pvar header lines now conform to VCFv4.3 specification (an ID field is included). VCF/BCF export now performs more header validation.
+
+16 Jan: --update-parents now works properly with 'maybeparents' output column sets in other commands.
+
+14 Jan: --update-ids now works properly with 'maybefid' output column sets in other commands when it creates a FID column.
+
+4 Jan: --normalize now properly skips missing and '*' alleles.
+
+3 Jan: Fixed --bcf bug that affected unphased multiallelic variants (usually resulting in a spurious "GT half-call" crash, but if you suppressed that with --vcf-half-call the data would not be imported correctly). Fixed "--export bcf" bug that occurred on headers with FILTER/INFO/FORMAT keys with identical names, and a crash that occurred on variants with multiple FILTER failures. --output-missing-genotype/--output-missing-phenotype bugfixes/cleanup.
+
+2 Jan: --pgen-diff multiallelic-variant handling bugfix. --pgen-diff DS comparison implemented. --adjust cols= parsing bugfix ('cols=+qq' should work now).
+
+1 Jan 2021: Several SID-handling bugfixes. --sample-diff 'dosage' and 'id-delim=' modifier command-line parsing bugfixes. --sample-diff no longer omits later ALT alleles when they're absent from the samples being compared. --pgen-diff GT comparison implemented (generalization of PLINK 1.x --merge-mode 6/7).
+
+12 Dec 2020: --q-score-range score-average, ALLELE_CT, DENOM, and NAMED_ALLELE_DOSAGE_SUM column bugfix.
+
+28 Oct: Multipass "--export A" bugfix. If you've previously run plink2 "--export A" on a file too large to fit in memory, we recommend that you rerun with this build.
 
 20 Oct: --fst Weir-Cockerham method implemented. --fst ids= and chrX bugfixes. --fst variant-report OBS_CT is now specific to population pair.
 



View it on GitLab: https://salsa.debian.org/med-team/plink2/-/commit/cce84c08bbabda72d56f0ef78c4056523175bb52

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View it on GitLab: https://salsa.debian.org/med-team/plink2/-/commit/cce84c08bbabda72d56f0ef78c4056523175bb52
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