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

[Dylan Aïssi (@daissi)]

Dylan Aïssi pushed to branch master at Debian Med / plink2


Commits:
92c9e36a by Dylan Aïssi at 2021-07-23T21:56:28+02:00
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 +1,39 @@
 # Copy/Paste from https://www.cog-genomics.org/plink/2.0/
 
-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.
+1 Jul 2021: Fixed --bcf bug that could result in a spurious out-of-memory error when the file has no INFO entries.
+
+8 Jun: Fixed multiallelic-variant-writing bug (typically manifesting as a segmentation fault or assertion failure) that could occur with --sort-vars or under low-memory conditions.
+
+25 May: .fa loader now tolerates blank lines. gzip files containing multiple streams or trailing garbage should be accepted again.
+
+23 May: Fixed FID+IID+SID loading (recent builds were giving an incorrect "SID column does not immediately follow IID column" error).
+
+5 May: Fixed --within bug introduced on 16 Jan.
+
+20 Apr: --het cols= should now work properly.
+
+16 Apr: --data/--gen now supports .gen files with 6 leading columns. This format can be exported with "--export oxford-v2".
+
+14 Apr: --pmerge-list should no longer be limited by the system's #-of-open-files cap.
+
+13 Apr: --glm local-covariate-handling bugfix. Fixed --pmerge[-list] bug that could cause the generated .pgen header to be invalid when multiallelic variants were present.
+
+6 Apr: --data/--sample now recognizes column type 'C' as a synonym for 'P' (continuous phenotype). (This build has an incorrect "6 Mar" datestamp; sorry about that.)
+
+28 Mar: --sample-counts chrX no-known-males bugfix.
+
+25 Mar: --pmerge[-list] .bim-handling bugfix.
+
+23 Mar: Unbreak --make-pgen + --sort-vars (this was broken by the 28 Feb build).
+
+2 Mar: --pmerge[-list] bugfixes (no longer segfaults when all variants are at different positions; if the output .pvar file already exists, it's deleted first instead of appended to; if an input file covers multiple chromosomes, there is no longer a likely assert failure; fixed some issues with merging of same-position same-ID variants).
+
+1 Mar: --pmerge-list-dir flag implemented (specifies a common directory prefix for all --pmerge-list entries).
+
+28 Feb: --pmerge[-list] can now be used for concatenation-like jobs.
+Note that it doesn't necessarily perform pure concatenation on a chromosome-split dataset: if two variants in a file have the same position and ID, they will be merged, in a way that's not compatible with 'split' multiallelic variants sharing a single ID (those must be merged with a dedicated 'join' operation, such as "bcftools norm -m +"). As a consequence, --pmerge[-list] defaults to erroring out when it detects such a split variant. One workaround is to use --set-all-var-ids to assign distinct IDs to each piece of the split variant.
+
+3 Feb: 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.
 



View it on GitLab: https://salsa.debian.org/med-team/plink2/-/commit/92c9e36a2464632d6e2562f77d971886c0bfd0a0

-- 
View it on GitLab: https://salsa.debian.org/med-team/plink2/-/commit/92c9e36a2464632d6e2562f77d971886c0bfd0a0
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