[med-svn] [Git][med-team/plink2][master] Update changelogs

[Dylan Aïssi]

Dylan Aïssi pushed to branch master at Debian Med / plink2


Commits:
d73f17bb by Dylan Aïssi at 2020-01-20T07:43:43+01:00
Update changelogs

- - - - -


2 changed files:

- debian/changelog
- debian/upstream.docs/upstream.changelog


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+plink2 (2.00~a3-200116+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream release.
+
+ -- Dylan Aïssi <daissi at debian.org>  Mon, 20 Jan 2020 07:41:03 +0100
+
 plink2 (2.00~a2-191128+dfsg-1) unstable; urgency=medium
 
   * Initial release. (Closes: #858947)


=====================================
debian/upstream.docs/upstream.changelog
=====================================
@@ -1,7 +1,29 @@
 # Copy/Paste from https://www.cog-genomics.org/plink/2.0/
 
-28 Nov 2019: Fixed a VCF half-call handling bug introduced last month.
-This is a candidate for the final alpha 2 build (which will remain available for download for several months).
+16 Jan 2020: --pca allele/variant weight multithreading bugfix.
+
+14 Jan: --make-king-table rel-check bugfix.
+
+3 Jan 2020: Fixed --extract-if-info/--exclude-if-info numeric-argument bug introduced in late October.
+
+30 Dec 2019 (alpha 3): This makes the following potentially compatibility-breaking changes:
+
+    --write-snplist and --indep-pairwise require all variant IDs to be unique. For --write-snplist, this can be overridden by adding the 'allow-dups' modifier.
+    .bgen/.gen import commands require the REF/ALT mode to be explicitly declared.
+    --glm defaults to 'firth-fallback' mode for binary phenotypes. The old behavior can be requested with the 'no-firth' modifier.
+    --glm errors out, instead of just skipping the phenotype and printing a warning, when there's a linear dependency between the phenotype and the covariates. The old behavior can be requested with the 'skip' modifier.
+    --pca's 'var-wts' subcommand has been replaced with 'allele-wts', which handles multiallelic variants properly. For datasets that contain only biallelic variants, the old output format can still be requested with 'biallelic-var-wts'.
+    PLINK 2 now errors out when you request an LD computation on a dataset with less than 50 founders. This can be overridden with --bad-ld.
+    --score's old NMISS_ALLELE_CT column (nonmissing allele count) has been renamed to ALLELE_CT, and the column set renamed accordingly, since in other contexts, 'nmiss' refers to the number of missing values, which is essentially the opposite...
+    --make-king-table's ID{1,2} columns have been renamed to IID{1,2}, for consistency with other PLINK 2 commands.
+
+In addition, the GRM computation (along with "--pca approx" and "--score variance-standardize") now handles multiallelic variants properly, instead of just collapsing all minor alleles together; --score allows each allele in a multiallelic variant to be assigned its own score; and --glm handles categorical covariates in a manner that's less likely to cause VIF overflow.
+
+29 Dec: Fixed a bug which affected processing of some heterozygous-double-ALT multiallelic variants, and a bug that caused ALT2/ALT3/etc. allele frequencies to not be properly initialized in some circumstances.
+
+13 Dec: Fixed bug introduced in 22 Nov build which caused some reported dosages/counts (such as --freq's OBS_CT column) to be doubled. --loop-cats bugfixes.
+
+28 Nov: Fixed a VCF half-call handling bug introduced last month.
 
 26 Nov: Fixed recent bug which caused a segfault when no-duplicate-allowed variant ID lookup was performed with more than 16 threads.
 



View it on GitLab: https://salsa.debian.org/med-team/plink2/commit/d73f17bbefd9693a4839f75e5c5ebd134cbf294b

-- 
View it on GitLab: https://salsa.debian.org/med-team/plink2/commit/d73f17bbefd9693a4839f75e5c5ebd134cbf294b
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200120/1e4aa15f/attachment-0001.html>