dos September: –amount ‘noheader’ is to now work properly whenever particular phenotypes is forgotten. –vcf + –vcf-filter out now parses semicolon-delimited Filter out fields correctly. –vcf-min-gq banner put into development make. –exclude/–pull not any longer enjoys terrible overall performance when the head dataset additionally the –exclude/–pull variant record provides millions of ‘.’ records.
twenty eight August: –recode HV[-1chr] now constantly spends ‘0’ since the forgotten phenotype password, once the Haploview doesn’t undertake -nine. –write-covar + –with-phenotype no more segfaults into the instance/manage phenotypes, and you can multichar allele .ped loader not any longer segfaults for the nonstandard tri/quadallelic alternatives. –meta-data placed into development generate.
14 August: Fixed good typo regarding eleven August create hence triggered covariate packing and a few other properties to hang.
eleven August: –linear/–logistic no longer spends a push chair Huber-Light standard error estimator when groups is defined. –output-chr now functions securely with –make-sleep in the event the enter in .bim was unsorted, and you may a long allele code inside the an enthusiastic unsorted .bim don’t reasons –make-sleep to help you segfault.
1 August: –serving logistic regression bugfix. –make-just-bim and you can –make-just-fam flags extra. .bim/.fam data may now be processed rather than an associated .bed lower than particular facts. –recode-allele now really works safely which have Good-transpose mode.
18 July: Text message filesets having both multi-character allele codes and you may an enthusiastic unsorted .chart document not result in the autoconverter so you’re able to freeze. –pfilter would be to now consistently filter out ‘NA’ records. –serving chromosome code efficiency insect fixed. –read-freq now plenty A1 allele rules when they are lost regarding the main dataset, instead of erroring call at one to state. –show-tags set in invention make.
First Cochran-Mantel-Haenszel and you will Breslow-Time evaluating put in invention create
cuatro July: Fixed two merge insects hence possibly caused study over the last couple examples of an insight otherwise matched fileset become mishandled. 90 alpha/beta generates, and more than a few examples were in it, i suggest redoing the new combine that have a newer make. (Very merges was unchanged, however, top safer than just sorry.)
When you have merged filesets produced that have earlier PLINK step 1
1 July: Enhance recently atheistische Dating-Seite introduced (disappointed about this) –data/–gen/–test demand-line parsing insect. –indep no longer misreports the amount of pruned variants whenever indeed there are comprehensive multicollinearity. –fst, –homog, and –oxford-pheno-term flags additional.
twenty-seven Summer: «–recode oxford» no longer dumps wrong IDs whenever used in an equivalent work with while the an example filter out. –fill-missing-a2 banner added. –recode ‘A-transpose’ and you may ‘include-alt’ modifiers additional. «–het brief-sample» setting additional.
20 Summer: Repaired –mendel zero chromosome password/segfault bug. –merge-number no more means a resource fileset. –fast-epistasis + –parallel bugfix. –indep-pairphase and you may QFAM shot finished in creativity build.
ten June: –merge-function step one today accurately merges forgotten calls with a single nonmissing telephone call. –r/–r2 chromosome border handling bugfixes. ‘0X’/’0Y’/’0M’ chromosome codes emitted of the Oxford products are now recognized, and then have backed by –output-chr. –vcf-half-call banner set in control management of ‘0/.’ VCF GT opinions, and you may standard behavior has started to become ‘error’ setting to force a mindful ent build.
5 June: –ld-snp-list and you can multipass –r/–r2 bugfixes. Nonstandard ‘0/.’ and you may comparable VCF GT community opinions are actually canned while the once they didn’t have this new trailing ‘/.’, instead of causing a good segfault. (Management of this situation is configurable later on, listen in.) –linear/–logistic permutation bugfix (permutation achievements matter variety wasn’t initialized to-zero). –serving linear regression set in development make.
3 Summer: Gzipper no more deletes this new yields file when being questioned in order to append (this was resulting in larger n-citation calculations such –r2 gz to only support the output of the history solution). Fixed –genome double-missing-label dealing with insect, and a –r/–r2 combined autosomal/nonautosomal data handling insect. «–amount are present» and you may –write-dosage set in development create.
e-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 further emits places about heading line. –reduces now has a great ‘no-pheno-req’ modifier which eliminates the excessive phenotype specifications. –annotate set in creativity create.