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bob.dybian-guest pushed a commit to branch master
in repository plink1.9.

commit 96d83fa8dd6ecc5648eb21450ad430bdb3210f95
Author: Dylan Aïssi <>
Date:   Sat Sep 17 10:40:16 2016 +0200

    Install an upstream changelog
 debian/rules              |   3 +
 debian/upstream.changelog | 269 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 272 insertions(+)

diff --git a/debian/rules b/debian/rules
index 40e6983..16e0f8d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -21,3 +21,6 @@ override_dh_auto_build:
        dh_installman plink1.9.1
+       dh_installchangelogs debian/upstream.changelog
diff --git a/debian/upstream.changelog b/debian/upstream.changelog
new file mode 100644
index 0000000..62677fa
--- /dev/null
+++ b/debian/upstream.changelog
@@ -0,0 +1,269 @@
+# Copy/Paste from
+10 Sep 2016: --remove-cluster-names + --family bugfix. 
--indep-pairwise/--indep-pairphase consistency improvements (MAF comparison now 
takes floating point imprecision into account; a few pairwise comparisons are 
no longer improperly skipped when the window is kb-based).
+16 Aug: --merge-x 'no-fail' modifier works properly again. 
'--hard-call-threshold random' bugfix for probabilities with less than 4-digit 
+5 Aug: --silent Windows bugfix. --r/--r2 'd' and 'dprime-signed' modes added. 
--ld-window-cm flag added. --output-missing-genotype now works properly with 
--make-bed. --genome + --read-freq bugfix.
+7 Jun: --23file X/Y/MT chromosome conversion bugfix. --pheno bugfix (if 
phenotype was quantitative, but first value was nonnumeric, it was treated as 
'0' instead of missing in recent builds).
+16 May: Set test bugfix. '--R debug' bugfix.
+31 March: '--split-x b38' now works properly. 32-bit set-test bugfix. 
--cluster + --within bugfix.
+25 March: --recode beagle bugfix. --gene bugfix. '--vcf-half-call reference' 
mode added.
+15 March: Fixed --update-alleles bug introduced in 24 Feb build.
+13 March: Fixed .lgen loading bug introduced in 24 Feb build. Fixed 
use-after-free bug in extra chromosome name cleanup code. 
--allow-no-{samples,vars,covars} added to stable build.
+24 February: Contig limit raised to ~65000. --annotate/--gene-report bugfix 
for 3-4 column case. --flip-scan bugfix.
+3 February: Number-to-string encoding bugfix (occasionally affected numbers ≥ 
106 saved in the .bim centimorgan column).
+27 January 2016: Speed improvement for operating on a subset of samples. Fix 
minor --1 backward compatibility break.
+24 December 2015: Fix --dosage + --extract/--exclude bug introduced in 4 
November build. Minor --test-missing permutation bugfix. --vcf-min-qual bugfix 
for .bcf files.
+16 December: '--meta-analysis + study qt' now reports regression betas instead 
of odds ratios in the study-specific columns. '--score header' no longer 
forgets to append .nopred to the problem list filename.
+13 December: --allow-no-samples and --allow-no-vars flags added. --dosage now 
suppresses regression results for very-low-MAF variants in the same same manner 
as it does in PLINK 1.07. --lgen flag now supported. --gxe works properly again 
(it was inadvertently disabled a few months ago). --hardy now produces 'nan' 
results for chrY/chrM variants (like PLINK 1.07) instead of entirely omitting 
them. --hwe 'observation counts' warning is no longer triggered by chrY 
variants, and is now more i [...]
+26 November: --logistic can now report intercepts. --logistic adaptive 
permutation bugfix. If you used adaptive permutation with --logistic in the 
past, we recommend that you redo the run with the latest build.
+22 November: --indep{-pairwise,-pairphase} kb-based windows now work properly 
with sample/variant filters. Several --indep-pairphase bugfixes. --all-pheno no 
longer causes exit code 127 to be returned on successful runs. --recode-allele 
segfault bugfix. --meta-analysis now only considers the first appearance when a 
variant appears multiple times in the same file. --no-const-covar and 
--meta-analysis-report-dups flags added.
+4 November: Fixed '--r{2} square0' bug which occasionally caused a line break 
to be missing in the middle of the output file. Fixed --genome + --parallel 
missing-data handling bug.
+17 October: Set-handling bugfixes. --{fast-}epistasis + variant filtering 
bugfix. --score 'double-dosage' modifier added.
+3 September: --{b}merge no longer crashes when two sample IDs are mostly 
identical but have different capitalization and different parental 
IDs/phenotypes. Errors and warnings are now printed to stderr instead of stdout 
(yes, this is overdue). --dfam implemented. --vcf now accepts '*' 
deletion-overlap alt allele codes (thanks to John Wallace).
+15 July: --freq case-control mode added, and analogous --dosage 
case-control-freqs modifier added. Fixed --homozyg .summary bug that occurred 
when variant filters were present. Revised heterozygous haploid warning to be 
clearer. --mendel 'summaries-only' modifier added. --R missing value bugfixes. 
--dosage 'skip2' now works properly.
+29 June: --attrib{-indiv} now handles multiple negative match conditions in 
the same manner as PLINK 1.07. --clump + variant filter bugfix. --lasso is now 
+25 June: Fixed --snps bug that could arise when two named variants had 
positions differing by exactly 1.
+17 June: X chromosome Mendelian error checking bugfixes. '--dosage Zout' 
+13 June: --mds-plot switched from eigendecomposition-based algorithm back to 
SVD, and the matrix diagonal is now properly double-centered. (Update, 15 June: 
you can now use the --mds-plot 'eigendecomp' modifier in the development build 
to request the eigendecomposition algorithm, with the centering bug fixed. It 
does have the virtue of being several times faster than SVD.)
+29 May: --vcf now won't error out on GATK 3.4 symbolic deletion alleles. 
--recode 'gen-gz' modifier (for gzipping of Oxford-format .gen output) added. 
--pca header bugfix. --meta-analysis long allele code bugfix.
+20 May: --make-grm-bin + --parallel is now permitted by the command-line 
parser. Fixed bug in 11 May build which broke parsing of --gen + --sample.
+11 May: Fix --meta-analysis bug introduced in 18 April build. "Options in 
effect:" printed to standard output again, by popular demand.
+3 May: Merge + chromosome filter bugfix.
+18 April: --linear + --tests bugfix. --dosage + --exclude bugfix.
+9 April: --fst now works properly with variant filters.
+30 March: Fixed recent --dosage association report bug which caused null 
characters to appear on 'NA' lines. --linear/--logistic sex modifier + 
--parameters bugfix. (Update, 2 April: Linux binaries should no longer fail 
with "kernel too old" on RHEL 6 and similar systems.)
+18 March: --meta-analysis no-map bugfix, QFAM sibship handling bugfix.
+12 March: --mendel + --mendel-duos bugfix, --linear/--logistic + --adjust 
works properly again (--adjust was reporting "zero valid tests" when nothing 
was actually wrong). Missing genotype calls at otherwise monomorphic loci in 
multichar-allele .ped files are now converted properly (they were previously 
encoded as a pair of '0' alleles, instead of a missing call). QFAM test closed 
for repairs. --distance-wts partially added to development build (GRM variant 
weighting coming soon).
+5 March: --fast-epistasis 32-bit missing data handling bugfix. --thin-indiv 
and --thin-indiv-count added to development build (courtesy of Masahiro Kanai).
+2 March: VCF 'PR' header line is no longer malformed. (Existing malformed VCFs 
generated by January-February builds can be fixed by adding a '>' at the end of 
that line.) Fixed a set-handling bug that could affect sets containing the 
dataset's last variant.
+26 February: '--recode vcf' header modified for compatibility with VCFtools. 
Compact 1000 Genomes phase 1 data files posted on the resources page.
+10 February: Low-memory --r/--r2 matrix output bugfix. --recode vcf can now 
generate bgzipped output. More gzip/bgzip multithreading.
+2 February: --bcf now handles BCFv2.2 nonzero missing genotype and 
end-of-vector values (emitted by e.g. bcftools 1.1) properly. --mendel-multigen 
is no longer blocked by the command-line parser when a family-based association 
test is run. Oxford-format import now tolerates identical A1/A2 allele codes. 
--missing, --freq, --hardy, and --het now support gzipped output (add the 'gz' 
modifier). --R added to development build.
+15 January: --keep/--remove now works properly on newly-updated IDs when 
--update-ids is in the same run. --mac/--max-mac added to development build.
+12 January: --dosage + --covar + --sex now works properly, and an inaccurate 
warning about the PLINK 1.07 implementation has been removed. --dosage logistic 
regression no longer reports improper p-values for very small samples.
+11 January 2015 (beta 3): --epistasis implemented, with heavy optimization for 
quantitative traits. '--recode vcf{-fid/-iid}' now flags reference alleles as 
"possibly not based on a real reference genome" unless --real-ref-alleles is 
also specified, and sets ALT alleles to '.' when they are not present in the 
immediate dataset. --vcf-min-gq and --vcf-min-gp no longer error out when a 
genotype entry has fewer fields than expected, since the VCF specification 
explicitly states that this is [...]
+20 December 2014: --dummy, --show-tags, --neighbour, --mh/--bd/--mh2/--homog 
and --clump-field bugfixes. --q-score-range implemented for dosage data. 
--split-x/--merge-x 'no-fail' modifier added to support data conversion scripts.
+13 December: Case/control --hardy/--hwe no longer randomly excludes too many 
controls from control-only stage of test. (This was mostly harmless, since the 
all-samples test still worked, and the bug was only likely to occur when 
--hardy/--hwe was in the same run as other filters like --exclude/--extract. 
But if you used the UNAFF rows in the --hardy report for anything, you should 
rerun --hardy with the latest build.) set-test multiple-testing correction now 
counts nonempty sets with zer [...]
+11 December: --dosage format=3 + --score bugfix. 'beagle-nomap' option added 
to --recode. --list-duplicate-vars flag added to development build.
+7 December: --adjust now applies to the joint test statistic instead of the 
additive effect when the former is computed, and no longer reports linearly 
genomic-controlled p-values when they would be invalid. Some numeric stability 
improvements for small p-values. --logistic permutation test and 
--assoc/--model set-test bugfixes. --linear/--logistic set-test and --dosage 
'sex' modifier implemented. --dosage + --sex error message now explains that 
PLINK 1.07 did not handle this flag combin [...]
+25 November: Fixed --exclude/--extract memory management bug in 2 November 
build. --score now supports dosage data. --write-dosage no longer writes 
incorrect IDs when sample filters are applied. --dosage 'noheader' can now be 
used with 'list' when each batch has only one file. --assoc/--model set-test 
implemented. --set-missing-var-ids extended to permit inclusion of allele 
names, and --set-missing-snp-ids/--set-missing-nonsnp-ids retired. UNADJ column 
values are now correct in '--adjust [...]
+2 November: Improved variant ID lookup speed. Single-precision binary matrix 
output (e.g. --make-grm-bin) is now based on double-precision internal 
computations, and the 'bin' + 'single-prec' modifier combination has been 
replaced with 'bin4'. Binary --distance output bugfix.
+15 October: Fixed a bug in --vcf's handling of variants with 10 or more 
alternate alleles. --dosage Zout no longer segfaults at the end. Merger no 
longer scrambles centimorgan coordinates.
+26 September: Fixed --nonfounders bug which broke X chromosome MAF 
computation. --vcf-min-gp now tolerates '?' GP values.
+20 September: Fixed non-strict --biallelic-only bug when handling multiallelic 
variants. If you have used --biallelic-only without 'strict' on VCF files with 
triallelic variants, we strongly recommend rerunning the operation with the 
latest build. Fixed quantitative trait --assoc bug that caused it to write each 
output line twice, and --linear/--logistic mishandling of some datasets with 
heterozygous haploid calls. --vcf-min-gp added to development build.
+18 September: --no-fid bugfix. Presence of nonnumeric phenotype strings (e.g. 
'NA') no longer force the phenotype to be treated as quantitative. 
--output-missing-phenotype now accepts nonnumeric strings. '--dosage list' now 
works properly with multiple batches. --oxford-single-chr flag added to allow 
loading of single-chromosome .gen files with ignorable SNP ID field values. 
--genome no longer fails to report some parent-offspring relationships. 
--update-alleles was still missing a few m [...]
+8 September: --write-dosage bugfix for 2730+ samples. --{b}merge/--merge-list 
now usually errors out when combined with a filter flag that wouldn't take 
effect. --meta-analysis now supports weighted Z-score-based analysis.
+2 September: --dosage 'noheader' should now work properly when some phenotypes 
are missing. --vcf + --vcf-filter now parses semicolon-delimited FILTER fields 
correctly. --vcf-min-gq flag added to development build. --exclude/--extract no 
longer have terrible performance when both the main dataset and the 
--exclude/--extract variant list have millions of '.' entries.
+28 August: --recode HV{-1chr} now always uses '0' as the missing phenotype 
code, since Haploview does not accept -9. --write-covar + --with-phenotype no 
longer segfaults on case/control phenotypes, and multichar allele .ped loader 
no longer segfaults on nonstandard tri/quadallelic variants. --meta-analysis 
added to development build.
+17 August: Fixed a recent library function bug which broke --filter, --within, 
and a few other flags.
+14 August: Fixed a typo in the 11 August build which caused covariate loading 
and a few other functions to hang.
+11 August: --linear/--logistic no longer uses a buggy Huber-White standard 
error estimator when clusters are defined. --output-chr now works properly with 
--make-bed when the input .bim is unsorted, and a very long allele code in an 
unsorted .bim no longer causes --make-bed to segfault.
+1 August: --dosage logistic regression bugfix. --make-just-bim and 
--make-just-fam flags added. .bim/.fam files can now be processed without an 
accompanying .bed under some circumstances. --recode-allele now works properly 
with A-transpose mode.
+18 July: Text filesets with both multi-character allele codes and an unsorted 
.map file no longer cause the autoconverter to crash. Malformed files generated 
by some old merges no longer cause segfaults. --pfilter should now consistently 
filter out 'NA' entries. --dosage chromosome code output bug fixed. --read-freq 
now loads A1 allele codes when they're missing from the main dataset, instead 
of erroring out in that situation. --show-tags added to development build.
+4 July: Fixed two merge bugs which potentially caused data in the last few 
samples of an input or merged fileset to be mishandled. If you have merged 
filesets generated with earlier PLINK 1.90 alpha/beta builds, and more than two 
samples were involved, we suggest redoing the merge with a more recent build. 
(Most merges were unaffected, but better safe than sorry.)
+3 July (beta 2): .ped file parser now properly handles --missing-genotype 
flag. --mh2 implemented.
+1 July: Fix recently introduced (sorry about that) --data/--gen/--sample 
command-line parsing bug. --indep no longer misreports the number of pruned 
variants when there is extensive multicollinearity. --fst, --homog, and 
--oxford-pheno-name flags added.
+27 June: '--recode oxford' no longer dumps incorrect IDs when used in the same 
run as a sample filter. --fill-missing-a2 flag added. --recode 'A-transpose' 
and 'include-alt' modifiers added. '--het small-sample' mode added. Basic 
Cochran-Mantel-Haenszel and Breslow-Day tests added to development build.
+20 June: Fixed --mendel zero chromosome code/segfault bug. --merge-list no 
longer requires a reference fileset. --fast-epistasis + --parallel bugfix. 
--indep-pairphase and QFAM test completed in development build.
+10 June: --merge-mode 1 now correctly merges missing calls with a single 
nonmissing call. --r/--r2 chromosome boundary handling bugfixes. '0X'/'0Y'/'0M' 
chromosome codes emitted by Oxford tools are now recognized, and also supported 
by --output-chr. --vcf-half-call flag added to govern handling of '0/.' VCF GT 
values, and default behavior is now 'error' mode to force a conscious decision. 
--dosage completed in development build.
+5 June: --ld-snp-list and multipass --r/--r2 bugfixes. Nonstandard '0/.' and 
similar VCF GT field values are now processed as if they did not have the 
trailing '/.', instead of causing a segfault. (Handling of this case may be 
configurable in the future, stay tuned.) --linear/--logistic permutation bugfix 
(permutation success count array was not initialized to all-zero). --dosage 
linear regression added to development build.
+3 June: Gzipper no longer deletes the output file when being asked to append 
(this was causing big n-pass calculations such as --r2 gz to only keep the 
output of the last pass). Fixed --genome double-missing-call handling bug, and 
a --r/--r2 mixed autosomal/nonautosomal data handling bug. '--dosage occur' and 
--write-dosage added to development build.
+28 May: Fixed a few nonstandard chromosome name-related segfaults. '--r2 
dprime' missing data handling bugfix. Corrected misnamed 
--filter-attrib{-indiv} flags to --attrib{-indiv}, fixed a positive matching 
bug, and added support for gzipped attribute files. '--recode A{D} tab' no 
longer emits spaces in the header line. --blocks now has a 'no-pheno-req' 
modifier which removes the unnecessary phenotype requirement. --annotate added 
to development build.
+24 May: Sample-major to variant-major .bed transposition bugfix. Merger now 
provides an informative error message when given an sample-major .bed file, and 
does not log equal-position warnings when multiple variants have bp coordinate 
0 (since that's often used to indicate that the variant is unlocalized). 
--make-bed no longer crashes on tiny nonzero centimorgan coordinates. Contig 
limit raised to ~5000, to support draft mosquito genomes. --gene-report added 
to development build.
+20 May: 32-bit X/Ychr MAF calculation bugfix. --qual-scores added to 
development build.
+13 May: --logistic + sex covariate bugfix. --snp without --window no longer 
behaves like --snp + '--window 0' when other variants share the same bp 
coordinate. --pca now errors out instead of returning all-zero 
eigenvalues/vectors when samples with no genotype data are present.
+11 May (beta 1): Fast third-party --logistic code integrated (see credits page 
for details). Logging now permits gPLINK to consistently detect output files. 
--output-chr added. --family and --make-perm-pheno implemented. Within-cluster 
permutation bugfix. --linear/--logistic dominant/recessive models and covariate 
interactions work now. --tests bugfix.
+2 May: --clump-verbose no longer reports negative r2 values when phase flips.
+1 May: --clump-verbose + --clump-range bugfix.
+26 April: Fixed merge bug in 21 and 25 April builds.
+25 April: Old sample-major PLINK binary files are now detected correctly. 
Malformed input error messages now include line numbers.
+15 April: --bcf now adds 1 to variant coordinates, since its coordinates are 
defined to be 0-based while VCF is 1-based.
+14 April: --check-sex/--impute-sex no longer silently considers nonmissing Y 
genotype counts by default. --bcf now treats missing variant IDs as if they 
were equal to '.', instead of erroring out. Basic parent-of-origin test 
+8 April: Centimorgan position loading bugfix. --mendel error description 
formatting bugfix. --lambda bugfix. --adjust now prints and logs estimated 
genomic control lambda value. --keep{-fam}/--remove{-fam} input files with 
duplicate IDs now just trigger a warning instead of an error. 
--check-sex/--impute-sex now has a 'y-only' mode.
+5 April: --not-chr bugfix. '--recode fastphase' no longer defaults to 0/1 
allele codes (though they can still be requested with e.g. '--recode 01 
fastphase'). --hardy2/--hwe2 now invoke the mid-p adjusted versions of --hardy 
and --hwe, to reflect the original chi-square test's lack of conservative bias.
+4 April: Fixed --hardy bug that caused chromosome names and marker IDs to 
sometimes be merged on case/control data. --check-sex/--impute-sex now use Y 
chromosome data when it's present. --flip-subset, --flip-scan, and basic exact 
binomial test --tdt implemented.
+28 March: Fixed --bcf bug that caused it to fail whenever there were multiple 
FORMAT fields. --score missing phenotype output bugfix.
+27 March: Fixed --bcf header line parsing bug (loading should no longer fail 
when the GT header line appears after a non-PASS INFO or FILTER line, and 
--vcf-filter should now work with BCF2 files). --split-x 'hg20' build code 
corrected to 'hg38'. --ibc Fhat2/Fhat3 bugfix. --het and --set-me-missing 
+26 March: --hardy/--hwe X chromosome case/control bugfix. --extract/--exclude 
now considers every token in a file, instead of just the first on each line 
(this was undocumented PLINK 1.07 behavior).
+25 March: --bcf no longer fails to load newer bcftools-generated files with 
'IDX=' toward the end of the GT meta-information line. File import shortcuts 
(--vcf + --out without --make-bed, etc.) now error out when a filter flag that 
wouldn't take effect (e.g. --extract, --hwe, --snps-only...) is specified. --me 
and --mendel implemented; --mendel-duos and --mendel-multigen flags added to 
extend their functionality. Fixed PLINK 1.07 --mendel issue where genotypes 
would be set to missing bef [...]
+22 March: --ld-snp-list long file bugfix, PLINK 1.07 --score Y chromosome 
handling bugfix.
+20 March: --condition-list command line parsing bugfix, --recode beagle 
bugfix, --make-founders bugfix, sample filtering bugfix for --regress-distance 
and --recode lgen/list/rlist. Basic --score implemention. Ueki/Cordell 
joint-effects test now skips marker pairs with less than 5 observations in any 
contingency table cell (where cases and controls are considered separately); 
this threshold is adjustable with --je-cellmin.
+17 March: --vcf-idspace-to flag added to improve handling of VCF/BCF2 sample 
ID spaces. --blocks is now more customizable.
+15 March: Multiple solutions to the haplotype frequency cubic equation (which 
arises when evaluating Lewontin's D-prime) should now always be handled 
correctly; there were a few corner cases which were mishandled before. Markers 
with identical bp coordinates no longer cause 1.9 --blocks to yield different 
results than 1.07 --blocks.
+14 March: --blocks implemented. D-prime computations ('--r2 dprime', --ld, 
--blocks, --clump) involving variants on the X chromosome now appropriately 
downweight males relative to females. --vcf and --bcf now handle sample ID 
spaces in a reasonable manner.
+7 March: Fixed minor --genome bug that clipped Z2 estimate to 0 instead of 1 
when it was too large. --all-pheno and --loop-assoc now print case/control 
counts for each phenotype.
+6 March: Fixed --make-bed bug that threw away major allele codes of 
monomorphic loci when the markers were unsorted and no minor allele code was 
+28 February: --a1-allele/--a2-allele 'fix' in 26 February build was backwards; 
this is no longer the case. If you used --a1-allele/--a2-allele from that build 
on a dataset with monomorphic loci and missing allele codes, you should 
download the latest build and rerun your pipeline from that point forward; 
sorry about the mistake. (We hope we were the only actual victims of this.) VCF 
importer now supports variants with 10+ alternate alleles.
+27 February: VCF generator no longer segfaults sometimes on the X chromosome. 
VCF allele code Nazi now just issues a warning, since some pipelines actually 
depend on violating the official spec.
+26 February: --a2-allele succeeds instead of giving 'Impossible allele 
assignment' warnings when the A1 allele code is unset, and vice versa for 
--a1-allele. Variant IDs in --a1-allele/--a2-allele 'Impossible allele 
assignment' warnings are no longer strangely truncated. VCF 'N' reference 
allele now handled in a saner manner (converted to and back from missing).
+25 February: --ci no longer prints incorrect confidence intervals with 
--linear/--logistic. --linear 'intercept' modifier and --thin-count added.
+24 February: Fixed .tped loading bug when original file was not fully sorted. 
VCF generator now forces the A2 (reference) allele to always be known, and 
outputs '.' instead of '0' when the A1 (alternate) allele is unknown; VCF 
allele codes are also forced to either only contain characters in 
{A,C,G,T,N,a,c,g,t,n} or start with '<'.
+20 February: --r/--r2 bugfixes.
+19 February: Fixed errors that occurred when using disallowed (via --chr-set, 
--dog, etc.) X/Y/XY/MT chromosome codes with --allow-extra-chr. --dog now 
permits mitochondrial data.
+15 February: Fixed --hardy segfault on datasets with no controls. 
--recode-allele now works properly (it was changing the header line without 
flipping allele counts before). --clump-best implemented.
+14 February: Fixed '--genome full' IBS0 column printing bug in 11 February 
build. --set-missing-{snp/nonsnp/var}-ids flags changed to use @ instead of ^ 
to mark the chromosome code's position, since ^ is a reserved Windows shell 
character. --cm-map flag changed to also use @ for the chromosome code. 
LD-based result clumping (--clump) is now supported. --r/--r2 'in-phase' 
+11 February: Fixed --geno bug introduced in 23 January build 
(missing-phenotype samples were being partially thrown out for no reason). 
--set-missing-snp-ids and --set-missing-nonsnp-ids flags introduced, to handle 
the case of overlapping SNPs and indels being defined as separate variants at 
the same coordinate. --cow now permits mitochondrial data. 
Distance/relationship matrix calculations no longer waste a huge amount of time 
on thread creation and destruction when hundreds of cores ar [...]
+8 February: Thread limit temporarily decreased to 23, since higher numbers 
result in too much thread creation/destruction overhead for now. (This 
multithread efficiency issue will be solved in the near future.) Also see the 
major bugfix above.
+7 February: --genome + --parallel bugfix. --update-parents was broken in the 6 
February build; it should now be fixed, and now permits very long lines (so 
it's usable on .ped files).
+6 February: IDs and pedigree information are no longer incorrect when --genome 
is used with sample filtering flags. --extract/--exclude now support set range 
files (--range). Optional 'chr' chromosome prefixes may now be partly or 
entirely capitalized. --pca var-wts modifier, 
--pca-cluster-names/--pca-clusters projections. Gzipped and binary Oxford 
genotype files can now be directly imported. --update-sex now takes a column 
parameter (so it can be pointed directly at .ped/.fam files now).
+30 January: Fix --snps bug introduced in 23 Jan build. --pca, 
--set-missing-var-ids, --test-mishap. --aec is now acceptable shorthand for 
--allow-extra-chr. --rel-cutoff moved earlier in order of operations (so e.g. 
--rel-cutoff --make-bed works).
+26 January: --file now handles nonstandard chromosome names in .map files 
properly. --make-grm-bin + --parallel output filename fix. --test-missing 
max(T) permutation test.
+24 January: --covar-name fixed, hopefully for good. Fixed contig name handling 
bug which slipped into 23 Jan builds. Fisher mid-p adjustment + permutation 
test bugfix. --test-missing adaptive permutation test.
+23 January: Fixed a bug with --missing + sample filters, as well a minor PLINK 
1.07 --missing + --within bug. Contig limit raised to ~2500. --zero-cluster, 
--oblig-missing. --geno and --mind should now treat sex chromosomes the same 
way as PLINK 1.07.
+16 January: Oxford-format loader now accepts tab-delimited text files, because 
apparently that is a thing. --hwe interface improved (inappropriate default 
p-value removed, and a warning is now printed whenever observation counts vary 
by more than 10%).
+14 January: Fixed .bim sorting bug when some loci were simultaneously being 
filtered out. --check-sex and --impute-sex implemented. Hardy-Weinberg and 
Fisher's exact tests now support mid-p adjustments. Proper handling of 
ambiguous sex codes. Y chromosome 'nonmissing nonmale genotypes' warning no 
longer gets sexes backwards (oops). Mitochondrial DNA no longer required to be 
haploid (though there are no plans to support full polyploidy). --split-x and 
--merge-x flags added to simplify han [...]
+9 January: --all-pheno now includes phenotype IDs in output filenames when 
possible (instead of 'P1', 'P2', etc.). --hardy + variant filter bugfix. 
--linear/--logistic covariate handling bugfix. Support for SHAPEIT 
recombination maps added (--cm-map).
+7 January 2014: --indep{-pairwise} speed improvement in no-missing-call case. 
Cluster permutation and --covar-name range handling bugfixes. --snps-only 
filter added. Linux/OS X thread limit raised to 1023.
+23 December 2013: Oxford-format loader no longer requires 'missing' to be 
lowercase. Basic --test-missing. Fixed a bug which sometimes came up when using 
--ibs-test or association analysis commands while filtering out samples.
+21 December: Covariate loader bugfix.
+20 December: --condition-list bugfix, --bcf + --vcf-filter bugfix. 
--make-rel/--make-grm-gz/--make-grm-bin/--ibc work properly again when input 
file has some major alleles in the A1 position. (Also fixed the --distance 
segfault introduced in the 18 Dec build; sorry about that.)
+11 December: Fixed loading of .map files missing a centimorgan column. 
--fast-epistasis set-by-set works properly with two sets now.
+9 December: --r/--r2 dprime bugfixes, --fast-epistasis uninitialized N_SIG 
bugfix. Basic variant set file I/O, --fast-epistasis set-based tests.
+5 December: --make-bed position sort and Oxford-format loading bugfixes. 
32-bit --r/--r2/--fast-epistasis bugfix. --fast-epistasis now supports extended 
version of BOOST test (missing data permitted, df properly adjusted in the face 
of e.g. zero homozygous minor observations). --r/--r2/--ld finished. --gplink 
flag supported.
+26 November: --filter-nonfounders segfault fix.
+25 November: --biallelic-only segfault fix when 'list' modifier was not 
specified. BCF2 (either uncompressed or BGZF-compressed) and Oxford-formatted 
data can now be directly imported. --fast-epistasis now supports the 
Ueki-Cordell joint effects test, and fills the 3x3 contingency tables more 
quickly when no missing markers are present (increasing the speedup factor to 
~60C in that case). --fast-epistasis + --parallel works.
+17 November: --r/--r2 bugfix, --fast-epistasis, --recode oxford. (The 
--fast-epistasis implementation is roughly 40C times as fast as PLINK 1.07, 
where C is the number of processor cores, and it also employs a more accurate 
variance estimator.) A bit of dead wood trimmed to make way for better 
implementations (--regress-pcs, dosage distance calculator); let us know if you 
want those functions to return sooner rather than later.
+12 November: Basic VCF text loader. Add check for matching input and output 
filenames when using --rel-cutoff in batch mode.
+10 November: --r/--r2 square matrices. Fixed 
--keep/--remove/--extract/--exclude bug introduced in a recent build. --genome 
IBD sharing calculation bugfix. --indep{-pairwise} results should no longer be 
slightly discordant with PLINK 1.07 when missing data is present (standard 
deviations were previously calculated once per site, they're now recalculated 
for every pair).
+8 November: --indep{-pairwise} corner case bugfix. --filter-attrib{-indiv}.
+3 November: .ped loader should no longer run out of memory if a single very 
long allele is present.
+1 November: The main loading sequence and most functions should now handle 
very long allele names. .ped multi-character allele loading and 
--a1-allele/--a2-allele bugfixes.
+28 October: Fixed some merge and multichar allele handling bugs. --filter can 
now match against more than one value. Cluster membership filters added 
(--keep-clusters, --keep-cluster-names, --remove-clusters, 
+19 October: --lasso now supports covariates.
+17 October: --pheno missing quantitative phenotype bugfix, minor --lasso 
+16 October: Basic LASSO implementation (--lasso). --linear/--logistic X 
chromosome bugfix.
+14 October: --missing. Various --linear/--logistic bugfixes. 
--linear/--logistic permutation tests now correctly announce when they are 
employing multiple threads.
+13 October: --linear/--logistic. Nonautosomal chromosome filtering bugfix.
\ No newline at end of file

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