dos September: –dose ‘noheader’ is now work properly when specific phenotypes are shed. –vcf + –vcf-filter out now parses semicolon-delimited Filter areas truthfully. –vcf-min-gq banner added to advancement make. –exclude/–extract no longer has actually terrible overall performance whenever both chief dataset and –exclude/–pull variation list have many ‘.’ entries.
twenty-eight August: –recode HV[-1chr] today usually spends ‘0’ since shed phenotype code, as Haploview will not deal with -nine. –write-covar + –with-phenotype not any longer segfaults for the instance/control phenotypes, and you may multichar allele .ped loader no more segfaults towards nonstandard tri/quadallelic alternatives. –meta-study put in invention build.
fourteen August: Repaired a typo on the 11 August make and therefore brought about covariate loading and a few other qualities to hang.
11 August: –linear/–logistic no more spends a pram Huber-Light simple error estimator whenever clusters is defined. –output-chr today works properly with –make-sleep if type in .bim are unsorted, and you may a long allele code into the an unsorted .bim no further reasons –make-bed so you’re able to segfault.
step 1 August: –dose logistic regression bugfix. –make-just-bim and you can –make-just-fam flags additional. .bim/.fam documents is now able to be canned as opposed to an accompanying .sleep less than certain points. –recode-allele now work safely that have Good-transpose means.
18 July: Text message filesets that have each other multi-profile allele codes and you can an unsorted .map file not any longer result in the autoconverter so you can crash. –pfilter will be now consistently filter ‘NA’ entries. –serving chromosome password production bug repaired. –read-freq now lots A1 allele rules if they are missing regarding the fundamental dataset, in place of erroring call at one to disease. –show-tags set in development generate.
Very first Cochran-Mantel-Haenszel and you will Breslow-Day assessment put into creativity build
4 July: Fixed one or two mix pests and that probably caused study in the last partners samples of a feedback or merged fileset become mishandled. 90 leader/beta produces, and most a couple products have been involved, i recommend redoing the newest merge which have a newer create. (Really merges have been unaffected, but most readily useful safer than disappointed.)
When you yourself have matched filesets produced that have earlier PLINK step 1
step 1 July: Fix recently produced (disappointed about that) –data/–gen/–shot order-range parsing insect. –indep no more misreports how many pruned variants when indeed there was thorough multicollinearity. –fst, –homog, and –oxford-pheno-term flags additional.
27 June: “–recode oxford” not places completely wrong IDs whenever utilized in a similar focus on as the an example filter. –fill-missing-a2 flag added. –recode ‘A-transpose’ and you will ‘include-alt’ modifiers additional. “–het quick-sample” setting additional.
20 June: Repaired –mendel zero chromosome code/segfault bug. –merge-listing no further means a resource fileset. –fast-epistasis + –synchronous bugfix. –indep-pairphase and you can QFAM try finished in advancement create.
10 Summer: –merge-function 1 today accurately merges destroyed phone calls which have just one nonmissing call. –r/–r2 chromosome boundary addressing bugfixes. ‘0X’/’0Y’/’0M’ chromosome codes emitted by Oxford devices are siti web incontri viaggi actually recognized, and now have backed by –output-chr. –vcf-half-telephone call banner put into govern handling of ‘0/.’ VCF GT beliefs, and you can default choices happens to be ‘error’ means to make a mindful ent make.
5 Summer: –ld-snp-list and multipass –r/–r2 bugfixes. Nonstandard ‘0/.’ and you may similar VCF GT community philosophy are actually processed since the if they didn’t have this new trailing ‘/.’, in the place of ultimately causing a beneficial segfault. (Management of this case can be configurable later on, tune in.) –linear/–logistic permutation bugfix (permutation achievements matter range wasn’t initialized to-zero). –dosage linear regression put into creativity create.
3 June: Gzipper don’t deletes the fresh production file whenever are expected to append (this is ultimately causing huge letter-ticket data such as for instance –r2 gz to only contain the returns of the past pass). Repaired –genome double-missing-telephone call addressing insect, and you can good –r/–r2 mixed autosomal/nonautosomal data handling insect. “–dosage exists” and –write-amount set in development generate.
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” not produces spaces on header line. –reduces now has a good ‘no-pheno-req’ modifier and therefore removes the excessive phenotype criteria. –annotate set in development make.