Malformed documents created by particular dated merges no longer cause segfaults

2 Sep: –amount ‘noheader’ is to now work effectively whenever certain phenotypes is lost. –vcf + –vcf-filter today parses semicolon-delimited Filter sphere accurately. –vcf-min-gq banner put in creativity build. –exclude/–extract no more have terrible show whenever both main dataset as well as the –exclude/–extract variation checklist provides countless ‘.’ entries.

twenty-eight August: –recode HV[-1chr] now usually uses ‘0’ given that shed phenotype password, since Haploview doesn’t undertake -9. –write-covar + –with-phenotype no longer segfaults to your instance/control phenotypes, and multichar allele .ped loader no more segfaults on the nonstandard tri/quadallelic variations. –meta-investigation put into invention create.

14 August: Repaired good typo in the eleven August make and this triggered covariate loading and a few other services to hang.

eleven August: –linear/–logistic don’t spends a buggy Huber-White important error estimator when groups was defined. –output-chr today performs securely with –make-bed if enter in .bim is sitio de citas coreano actually unsorted, and you may a long allele code during the a keen unsorted .bim not any longer reasons –make-bed so you’re able to segfault.

1 August: –serving logistic regression bugfix. –make-just-bim and you may –make-just-fam flags extra. .bim/.fam records is now able to feel canned rather than an associated .sleep under certain circumstances. –recode-allele now functions properly which have A-transpose setting.

18 July: Text filesets that have both multiple-reputation allele requirements and you can an enthusiastic unsorted .map file not cause the autoconverter to help you crash. –pfilter is always to today constantly filter out ‘NA’ entries. –dosage chromosome code productivity bug repaired. –read-freq now plenty A1 allele rules when they are lost about head dataset, instead of erroring call at one condition. –show-labels set in development generate.

Very first Cochran-Mantel-Haenszel and you will Breslow-Day evaluation set in innovation generate

4 July: Repaired a few combine pests hence potentially caused studies during the last partners types of an insight or blended fileset to be mishandled. ninety alpha/beta creates, and more than a couple of trials had been with it, we suggest redoing this new combine that have a newer create. (Really merges had been unchanged, but greatest secure than just disappointed.)

When you yourself have combined filesets produced having before PLINK 1

step one July: Boost has just put (sorry about this) –data/–gen/–sample demand-line parsing bug. –indep no further misreports exactly how many pruned versions whenever around is actually thorough multicollinearity. –fst, –homog, and you can –oxford-pheno-term flags additional.

twenty seven June: “–recode oxford” not places wrong IDs when used in an equivalent work with once the a sample filter out. –fill-missing-a2 banner extra. –recode ‘A-transpose’ and you may ‘include-alt’ modifiers added. “–het brief-sample” form extra.

20 Summer: Fixed –mendel no chromosome password/segfault bug. –merge-list not need a resource fileset. –fast-epistasis + –synchronous bugfix. –indep-pairphase and you will QFAM sample completed in advancement generate.

10 Summer: –merge-mode step 1 today truthfully merges destroyed phone calls having a single nonmissing call. –r/–r2 chromosome line addressing bugfixes. ‘0X’/’0Y’/’0M’ chromosome requirements released of the Oxford devices are now recognized, while having supported by –output-chr. –vcf-half-phone call flag set in govern handling of ‘0/.’ VCF GT thinking, and you may default decisions has grown to become ‘error’ form to force a conscious ent make.

5 Summer: –ld-snp-record and you will multipass –r/–r2 bugfixes. Nonstandard ‘0/.’ and equivalent VCF GT job beliefs are in fact canned since the once they did not have the new behind ‘/.’, in the place of causing an effective segfault. (Handling of this situation are configurable subsequently, listen in.) –linear/–logistic permutation bugfix (permutation achievements matter array was not initialized to all the-zero). –dosage linear regression put in advancement make.

step three Summer: Gzipper not any longer deletes new returns document whenever becoming requested so you’re able to append (this was causing huge n-solution data instance –r2 gz to only keep the production of your own last admission). Repaired –genome twice-missing-label handling bug, and you will a good –r/–r2 combined autosomal/nonautosomal data-handling bug. “–amount exists” and you will –write-dosage put in creativity 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” no further produces room about header line. –stops is now offering a good ‘no-pheno-req’ modifier and that takes away the unnecessary phenotype requisite. –annotate put into advancement build.