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Malformed records generated by certain old merges no longer end up in segfaults

Malformed records generated by certain old merges no longer end up in segfaults

dos September: –amount ‘noheader’ is to today work properly when some phenotypes was lost. –vcf + –vcf-filter now parses semicolon-delimited Filter industries truthfully. –vcf-min-gq flag put into development build. –exclude/–pull not possess terrible efficiency when both main dataset together with –exclude/–pull variant listing enjoys many ‘.’ entries.

28 August: –recode HV[-1chr] today usually spends ‘0’ once the forgotten phenotype password, while the Haploview cannot undertake -9. –write-covar + –with-phenotype not any longer segfaults into case/manage phenotypes, and you may multichar allele .ped loader no further segfaults towards nonstandard tri/quadallelic variants. –meta-studies put in development build.

fourteen August: Fixed an excellent typo throughout the eleven August generate hence brought about covariate packing and a few other services to hang.

11 August: –linear/–logistic don’t uses a buggy Huber-Light basic mistake estimator whenever clusters are discussed. –output-chr now really works securely that have –make-sleep when the enter in .bim try unsorted, and a long allele code during the an enthusiastic unsorted .bim not reasons –make-sleep so you can segfault.

step one August: –dose logistic regression bugfix. –make-just-bim and you will –make-just-fam flags added. .bim/.fam data files may now getting canned in the place of an accompanying .sleep under some things. –recode-allele now really works securely which Dating mit einem chinesischen Mädchen have A-transpose form.

18 July: Text filesets that have one another multiple-reputation allele rules and you will a keen unsorted .map document no more result in the autoconverter to help you freeze. –pfilter is always to now continuously filter ‘NA’ records. –dose chromosome code returns insect repaired. –read-freq now loads A1 allele codes while they are forgotten regarding fundamental dataset, as opposed to erroring call at that state. –show-tags added to innovation build.

First Cochran-Mantel-Haenszel and you will Breslow-Time evaluating put into innovation create

4 July: Repaired a couple of blend pests and that possibly triggered studies during the last pair types of an input otherwise blended fileset are mishandled. ninety leader/beta generates, and more than two products have been on it, we recommend redoing this new combine with a newer create. (Extremely merges was indeed unaffected, however, best safe than sorry.)

When you yourself have merged filesets made that have earlier PLINK step 1

1 July: Improve has just lead (disappointed about this) –data/–gen/–try order-line parsing insect. –indep not misreports the amount of pruned versions whenever there is actually extensive multicollinearity. –fst, –homog, and you may –oxford-pheno-label flags additional.

27 Summer: «–recode oxford» no further deposits incorrect IDs whenever used in a comparable work at due to the fact an example filter out. –fill-missing-a2 flag extra. –recode ‘A-transpose’ and ‘include-alt’ modifiers additional. «–het quick-sample» means added.

20 Summer: Repaired –mendel zero chromosome code/segfault bug. –merge-checklist not any longer needs a reference fileset. –fast-epistasis + –parallel bugfix. –indep-pairphase and you will QFAM sample finished in advancement build.

ten June: –merge-mode step 1 now accurately merges destroyed calls with one nonmissing telephone call. –r/–r2 chromosome border dealing with bugfixes. ‘0X’/’0Y’/’0M’ chromosome requirements produced by Oxford units are actually approved, and also backed by –output-chr. –vcf-half-telephone call banner placed into control handling of ‘0/.’ VCF GT values, and standard behavior has become ‘error’ setting to make a conscious ent make.

5 Summer: –ld-snp-listing and you will multipass –r/–r2 bugfixes. Nonstandard ‘0/.’ and you will equivalent VCF GT job opinions are actually processed because if they did not have the latest behind ‘/.’, rather than resulting in an excellent segfault. (Handling of this example may be configurable in the future, listen in.) –linear/–logistic permutation bugfix (permutation achievements number variety was not initialized to-zero). –amount linear regression set in invention make.

step three June: Gzipper not deletes the fresh output file whenever getting expected in order to append (this is leading to large n-admission computations such as for example –r2 gz to only hold the yields of your own history pass). Fixed –genome twice-missing-call addressing insect, and you can a great –r/–r2 combined autosomal/nonautosomal data handling bug. «–amount can be found» and you can –write-dose set in advancement make.

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 any longer gives off places on heading line. –blocks now has a great ‘no-pheno-req’ modifier and that removes the excessive phenotype requisite. –annotate placed into advancement generate.