Malformed documents created by specific dated merges no more end up in segfaults

Malformed documents created by specific dated merges no more end up in segfaults

dos Sep: –amount ‘noheader’ is now sitio de citas para personas travesti work effectively whenever some phenotypes is forgotten. –vcf + –vcf-filter today parses semicolon-delimited Filter areas accurately. –vcf-min-gq banner placed into invention create. –exclude/–extract no further provides terrible overall performance when the head dataset therefore the –exclude/–pull version record possess an incredible number of ‘.’ records.

twenty eight August: –recode HV[-1chr] today always spends ‘0’ just like the missing phenotype code, because the Haploview cannot deal with -9. –write-covar + –with-phenotype don’t segfaults on instance/handle phenotypes, and multichar allele .ped loader no further segfaults to your nonstandard tri/quadallelic alternatives. –meta-investigation set in innovation create.

14 August: Fixed good typo throughout the eleven August generate and therefore triggered covariate loading and a few almost every other services to hang.

11 August: –linear/–logistic no longer spends a buggy Huber-White important error estimator whenever clusters try laid out. –output-chr now performs properly which have –make-sleep in the event that type in .bim was unsorted, and you can a very long allele code from inside the a keen unsorted .bim don’t grounds –make-bed to segfault.

step one August: –dosage logistic regression bugfix. –make-just-bim and you will –make-just-fam flags added. .bim/.fam records is now able to be processed without an accompanying .bed lower than some factors. –recode-allele now work securely which have A-transpose function.

18 July: Text message filesets with both multi-profile allele codes and an unsorted .map file no longer cause the autoconverter to help you crash. –pfilter would be to today constantly filter ‘NA’ entries. –dosage chromosome password production insect fixed. –read-freq now plenty A1 allele codes when they are missing regarding main dataset, instead of erroring out in you to definitely disease. –show-labels put in development make.

Earliest Cochran-Mantel-Haenszel and you will Breslow-Day tests put in innovation build

4 July: Fixed a couple blend bugs hence probably caused data during the last couples types of an insight otherwise matched fileset to-be mishandled. 90 leader/beta builds, and most a couple samples had been involved, i suggest redoing the fresh mix having a newer create. (Very merges have been unaffected, however, ideal safer than just sorry.)

For those who have blended filesets made which have earlier PLINK 1

step 1 July: Fix has just lead (disappointed about this) –data/–gen/–decide to try order-line parsing insect. –indep not any longer misreports just how many pruned versions when truth be told there are comprehensive multicollinearity. –fst, –homog, and you will –oxford-pheno-identity flags additional.

twenty-seven Summer: “–recode oxford” not deposits incorrect IDs when used in an identical focus on because a sample filter. –fill-missing-a2 banner extra. –recode ‘A-transpose’ and you can ‘include-alt’ modifiers extra. “–het small-sample” means added.

20 June: Repaired –mendel no chromosome code/segfault insect. –merge-number no further needs a reference fileset. –fast-epistasis + –synchronous bugfix. –indep-pairphase and QFAM attempt finished in development build.

10 June: –merge-function step one now precisely merges destroyed calls which have a single nonmissing name. –r/–r2 chromosome boundary approaching bugfixes. ‘0X’/’0Y’/’0M’ chromosome requirements produced of the Oxford units are actually accepted, as well as have backed by –output-chr. –vcf-half-phone call banner placed into govern handling of ‘0/.’ VCF GT viewpoints, and you can standard conclusion is ‘error’ setting to force a mindful ent build.

5 June: –ld-snp-listing and you will multipass –r/–r2 bugfixes. Nonstandard ‘0/.’ and you may equivalent VCF GT industry viewpoints are actually processed because the whenever they did not have the fresh behind ‘/.’, in lieu of leading to a beneficial segfault. (Handling of this situation is configurable in the future, tune in.) –linear/–logistic permutation bugfix (permutation achievement number variety wasn’t initialized to any or all-zero). –amount linear regression set in creativity create.

step three Summer: Gzipper no longer deletes the production document whenever being expected to append (it was leading to huge n-citation data such as –r2 gz to simply support the efficiency of past solution). Repaired –genome double-missing-label approaching insect, and you will a great –r/–r2 combined autosomal/nonautosomal data handling bug. “–dose are present” and you can –write-dosage added to invention 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 gives off room regarding the header line. –prevents is now offering a great ‘no-pheno-req’ modifier hence takes away the excessive phenotype specifications. –annotate placed into innovation create.

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