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22 November: --indep 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. 21 May: "--linear interaction sex" and "--logistic interaction sex" now work properly when no covariates are present. --tucc added to development build. 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. 21 Feb: "--indiv-sort file" no longer scrambles the phenotypes when used with --[b]merge or --merge-list. 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 or start with ' . Calculations which account for the additional information in the new file format. We will eventually look into GPU acceleration of the most commonly used slow operations. 9 Jan 2018: --all-pheno no longer gets into an infinite loop when one phenotype is all-missing. 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. 3 May: Merge + chromosome filter bugfix. 11 May: Fix --meta-analysis bug introduced in 18 April build. "Options in effect:" printed to standard output again, by popular demand. 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. 17 October: Set-handling bugfixes. --[fast-]epistasis + variant filtering bugfix. --score 'double-dosage' modifier added. 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. 15 March: Fixed --update-alleles bug introduced in 24 Feb build. 25 March: --recode beagle bugfix. --gene bugfix. "--vcf-half-call reference" mode added. 3 February: Number-to-string encoding bugfix (occasionally affected numbers ≥ 10 6 saved in the .bim centimorgan column). red flags will not be supported by the final 1.90 release. We recommend migrating away from PLINK 1 here, but if that's not practical, keep a permanent copy of the PLINK 1.07 binary around and modify the relevant lines of your scripts to explicitly refer to it. 17 Jul: Fixed uninitialized --make-set-border value bug. 3: We believe this now has almost no practical value, since the file format it expects is too different from VCF. 4: This was not fully developed in PLINK 1.07, and has been superseded by other IBD analysis packages. 5: PLINK's haplotype phasing and imputation algorithms are obsolete. Future PLINK versions will be able to import phase and dosage information emitted by other programs; the haplotype association commands will be reintroduced when that functionality is in place. Until then, BEAGLE 3.3 should be more accurate than PLINK for case/control haplotype association. 6: Free database software handles these operations in a more flexible and powerful manner. 7: Just use gzip / gunzip for this. Or better, pigz / unpigz . 5000, to support draft mosquito genomes. --gene-report added to development build. 20 Dec 2017: --meta-analysis 'report-all' now reports original stats instead of 'NA' when N=1. Fixed an inaccuracy in --adjust's handling of very small p-values. --make-just-fam works properly with just .fam input again. 1 May: --clump-verbose + --clump-range bugfix. 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.) 25 February: --ci no longer prints incorrect confidence intervals with --linear/--logistic. --linear 'intercept' modifier and --thin-count added. 24 February: Contig limit raised to. 13 January 2017: --ld-snps now works properly with other variant filters. --set-mixed-mt-missing flag added. 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. 14 August: Fixed a typo in the 11 August build which caused covariate loading and a few other functions to hang. Limitations. 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. PLINK's primary job is management and analysis of position-based SNP-like data for thousands of samples, and it is optimized for this setting. Here are a few things PLINK will probably never be able to do, since they are serious jobs best handled with fundamentally different data structures than the ones PLINK is built around. 17 Jun: --loop-assoc now works properly when the original .fam file has missing phenotype values. 7 Oct: Fixed corner-case (two of the four haplotypes have no known observations) bug in --ld/--r2/--blocks/--clump's statistical phasing procedure. 32-bit build can now sort >2GB .bed files without crashing. --annotate and --gene-report now work with --allow-extra-chr. We are primarily interested in the following three types of feedback during the current testing phase: 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. Note to testers. 1: Solaris is no longer explicitly supported, but it should be able to run the Linux binaries. 2: These are just mirrors of the binaries posted at http://zzz.bwh.harvard.edu/plink/download.shtml. 17 June: X chromosome Mendelian error checking bugfixes. "--dosage Zout" bugfix. 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.) 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. 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. 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 zero significant variants. 25 June: Fixed --snps bug that could arise when two named variants had positions differing by exactly 1. 31 March: "--split-x b38" now works properly. 32-bit set-test bugfix. --cluster + --within bugfix. 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. 15 April: --bcf now adds 1 to variant coordinates, since its coordinates are defined to be 0-based while VCF is 1-based. 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.) 7 May: --r/--r2 + variant filter bugfix. 26 September: Fixed --nonfounders bug which broke X chromosome MAF computation. --vcf-min-gp now tolerates '?' GP values. Build Operating system 1 Stable (beta 6.13, 30 Nov) Development (30 Nov) Old 2 (v1.07) Linux 64-bit download download download Linux 32-bit download download download macOS (64-bit) download download download Windows 64-bit download download download Windows 32-bit download download. 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 combination properly. Recent version history. 20 March (beta 4): --pca var-wts now reports allele codes. Minor statistical phasing bugfix. --[max-]mac, --R, and --thin-indiv[-count] no longer classified as unstable. PLINK 2.0 alpha builds are now available. 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. 16 August: --merge-x 'no-fail' modifier works properly again. "--hard-call-threshold random" bugfix for probabilities with less than 4-digit precision. 7 Aug: --assoc set-test bugfix. 9 May: --tests now works properly on MT and haploid chromosomes. Improved --score compatibility with v1.07 and v2.0. 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. 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. --> green flags are supported by the latest development build. You're more than welcome to try the new implementations; just make sure to check some of your results against PLINK 1.07 if you do so. red flags will not be supported by the final 1.90 release. We recommend migrating away from PLINK 1 here, but if that's not practical, keep a permanent copy of the PLINK 1.07 binary around and modify the relevant lines of your scripts to explicitly refer to it. 24 Oct: Fixed uninitialized-variable bug in --dosage + --q-score-range. "--indep-pairwise 500kb . " works properly again (the previous build required a space before the 'kb'). Continue using PLINK 1.07 for most of these operations. However, be aware that. 3 Nov: --meta-analysis-snp-field and --meta-analysis-ess-field bugfixes. 13 Oct: "--freq counts" no longer gives reversed results when alleles have been flipped from the initial .bim/.bed order. Fixed --logistic bug that could cause spurious NA results. 12 Jun: "--assoc fisher"'s multiple testing corrections no longer treat zero-MAF variants as valid tests. 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 informative when only triggered by chrX variants. 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. 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. 28 March: Fixed --bcf bug that caused it to fail whenever there were multiple FORMAT fields. --score missing phenotype output bugfix. 25 April: Old sample-major PLINK binary files are now detected correctly. Malformed input error messages now include line numbers. Comments should generally be made in the plink2-users Google group. 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. 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. 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. 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. 18 March: --meta-analysis no-map bugfix, QFAM sibship handling bugfix. 7 June: --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). 17 August: Fixed a recent library function bug which broke --filter, --within, and a few other flags. 9 April: --fst now works properly with variant filters. 15 Feb: Logistic regression no longer reports intercept beta values when it's supposed to report odds ratios. Scientific notation can now be used for command-line integer parameters. 11 December: --dosage format=3 + --score bugfix. 'beagle-nomap' option added to --recode. --list-duplicate-vars flag added to development build. 26 April: Fixed merge bug in 21 and 25 April builds. 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. 30 March: --ld-snps bugfix. 27 January 2016: Speed improvement for operating on a subset of samples. Fix minor --1 backward compatibility break. 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). 2 Dec 2018: --set 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 implemented. 25 Jul: --lfile now works properly when the .map file has three columns. 28 May: Fixed --file triallelic-variant handling bug which occurred when the .map was unsorted. 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 implemented. 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. 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. 11 January 2015 (beta 3): --epistasis implemented, with heavy optimization for quantitative traits. "--recode vcf " 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 an acceptable way to represent trailing missing values. --make-bed no longer segfaults when resorting a file too large to fit in memory. 20 May: 32-bit X/Ychr MAF calculation bugfix. --qual-scores added to development build. 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. 17 March: --vcf-idspace-to flag added to improve handling of VCF/BCF2 sample ID spaces. --blocks is now more customizable. 15 Oct: A2 allele is now consistently reference on chr3 in our 1000 Genomes phase 1 downloads. As a general rule, you shouldn't expect to keep REF/ALT alleles straight with PLINK 1.x, but we tried to make A2 consistently reference in these files and still didn't quite succeed; sorry about that. (Why was this discovered now, more than 2.5 years after the fact? Because PLINK 2.0 now has a --ref-from-fa flag which can easily check for this type of error.) Binary downloads. 30 Nov 2019: "--recode rlist" no longer forgets to generate a .map file. 10 Apr: --zero-cluster command-line parsing bugfix. --mendel-multigen bugfix. 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. 14 Nov (beta 5): --file + --merge[-list] bugfix. This bug was much more likely to trigger if the first .map file was unsorted, but if you have the chance we recommend redoing any --file + --merge and --file + --merge-list multi-.ped merges performed with earlier plink 1.9 builds. (.bed merging was unaffected, and --merge-list without --file was practically never affected.) 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. 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. 4 Mar: Brackets in command-line help text are now used in a manner more similar to other tools. --tests now works properly when a numeric argument is 1 past the end. 13 November: --geno/--missing now treat heterozygous haploid calls as nonmissing; this is consistent with --mind, and PLINK 1.07's behavior with --recode/--make-bed active. They're now inconsistent with what PLINK 1.07 did without --recode/--make-bed ; use --make-bed + --set-hh-missing first if you want the old behavior. "--ci 0.95" no longer produces 'L94'/'U94' column names when plink gets unlucky with rounding. Minor --exclude/--extract/--flip bugfix for input files with no newline at the end. --qfam[-within] bugfix. --dosage 'sex' modifier now works properly when some samples have been filtered out (e.g. because some phenotypes were missing). The following documented PLINK 1.07 flags are not supported by 1.90 beta 6: 26 February: "--recode vcf" header modified for compatibility with VCFtools. Compact 1000 Genomes phase 1 data files posted on the resources page. 20 September: VCF export no longer erases an alt allele absent from the immediate dataset, due to a retroactive revision to the VCF specification. Fixed "--model gen" permutation testing bug. 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. 26 May (beta 6): --merge-equal-pos bugfixes. If you used --merge-equal-pos with .bed+.bim+.fam filesets where allele order may have differed between .bim files, or with any .ped+.map fileset at all, we recommend redoing that run. 10 Oct: Fixed --tdt parent-of-origin-analysis handling of chrX. 12 Oct: --snps/--exclude-snps no longer always includes other variants at the same positions as the variant(s) you named. PLINK 1.90 beta. Source code, compilation instructions, and the like are on the developer page. 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. Bug reports, obviously. Unexpected and unwanted incompatibilities with PLINK 1.07's interface count as bugs. (When making a bug report, plase include a supporting .log file.) Remarks on our documentation. We'll try to rewrite/redesign any parts that are confusing. New feature requests. This can range from little bits of interface cleanup, to full calculations which cannot currently be performed at satisfactory speed/scale with existing software. 28 Oct: --meta-analysis-se-field flag added, for interoperation with recent PLINK 2.0 logistic regression output (which uses a 'LOG(OR)_SE' field name to disambiguate the standard error's units). General analysis of structural variation. There are common subcases, such as small indels, which can sometimes be treated like SNPs, and PLINK 1.07 also had a small specialized CNV analysis module which we aren't dropping. But modern whole-exome and whole-genome sequencing technologies are capable of detecting exotic deviations from reference which are neither SNP- nor CNV-like, and these deviations can be clinically relevant. You should use a more flexible platform, such as PLINK/SEQ (which was explicitly designed to handle corner cases beyond PLINK's reach, and also has good metadata handling facilities), to investigate these. Anything relating to raw reads. As mentioned above, we plan to add support for probabilistic genotype calls in 2015-17, but you will still need to use other program(s) to generate those calls from SAM/BAM/etc. files. Directly expose a graphical user interface. Use a program like gPLINK for this. (If you wish to update gPLINK, we'd of course be happy to support your efforts.) Handle read-only queries, especially on a small subset of the samples, at near-optimal speed. The PLINK 1 binary file format is a simple, compact rectangular matrix. Aside from the unavoidable choice of major dimension (the format is "variant-major" and sorted by genomic position, so operations on small genomic regions are especially efficient, while operations on small sample subsets don't get much of a speedup), the format is workflow-agnostic; read-only operations are relatively fast, and writing a new fileset is also relatively fast. If you are done with data filtering/merging/etc. and will just perform read-only operations in the future, you can reorganize your data in a way which is slow to write but allows some queries to be even faster. This is the main idea behind Ryan Layer's GQT software; its use of a "sample-major" data representation and a different (MAF-based) variant order make it especially complementary to PLINK. If you'll be performing queries on genomic regions, you may want to look at Heng Li's BGT. 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. 10 September: --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 May: Set test bugfix. "--R debug" bugfix. 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 gc" reports. 2 May: --clump-verbose no longer reports negative r 2 values when phase flips. 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). 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. 10 February: Low-memory --r/--r2 matrix output bugfix. --recode vcf can now generate bgzipped output. More gzip/bgzip multithreading. 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. 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 memory-efficient. 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. 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. 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. 65000. --annotate/--gene-report bugfix for 3-4 column case. --flip-scan bugfix. 15 Aug: --lasso should now work properly when there are samples with all covariates present but the main phenotype missing. 17 November 2016: chrX and chrY are no longer mishandled with --chr-set. 3 July (beta 2): .ped file parser now properly handles --missing-genotype flag. --mh2 implemented. 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 matches involving missing genotypes; this has been fixed. 22 March: --ld-snp-list long file bugfix, PLINK 1.07 --score Y chromosome handling bugfix. 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. 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. This is a comprehensive update to Shaun Purcell's PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling, the Purcell Lab, and others. (What's new?) (Credits.) (Methods paper.) 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 present. 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). 18 April: --linear + --tests bugfix. --dosage + --exclude bugfix. 25 March: --bcf no longer fails to load newer bcftools-generated files with ' 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 before scanning was complete (i.e. if there were overlapping trios, PLINK 1.07 could fail to report some errors). 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 August: --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. 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 March: Fixed .lgen loading bug introduced in 24 Feb build. Fixed use-after-free bug in extra chromosome name cleanup code. --allow-no- added to stable 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 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. 13 Sep: Improved logistic regression convergence-failure detection (affects case/control --epistasis as well as --logistic). Fixed --R memory leak. 13 February: --R now works properly with missing covariate entries. --epistasis + variant filter bugfix.

 

 

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