Malformed data files created by some dated merges don’t cause segfaults

Malformed data files created by some dated merges don’t cause segfaults

Malformed data files created by some dated merges don’t cause segfaults

dos September: –serving ‘noheader’ is today work properly whenever specific phenotypes try missing. –vcf + –vcf-filter out today parses semicolon-delimited Filter out fields truthfully. –vcf-min-gq banner put in development generate. –exclude/–extract not possess awful overall performance when the fundamental dataset and –exclude/–extract version checklist features an incredible number of ‘.’ entries.

twenty eight August: –recode HV[-1chr] now usually uses ‘0’ as lost phenotype code, once the Haploview does not take on -9. –write-covar + –with-phenotype not segfaults for the situation/manage phenotypes, and you can multichar allele .ped loader not segfaults on the nonstandard tri/quadallelic variations. –meta-data set in development make.

14 August: Fixed an effective typo regarding the eleven August create hence brought about covariate packing and some almost every other functions to hold.

11 August: –linear/–logistic not uses a buggy Huber-White simple mistake estimator whenever clusters was laid out. –output-chr now work properly which have –make-bed in the event that input .bim is actually unsorted, and you will a long allele code inside an unsorted .bim not any longer reasons –make-sleep to segfault.

step one August: –dosage logistic regression bugfix. –make-just-bim and you may –make-just-fam flags added. .bim/.fam documents is now able to be processed as opposed to an associated .sleep below some products. –recode-allele now performs securely which have A good-transpose form.

18 July: Text filesets which have each other multi-character allele requirements and you may an enthusiastic unsorted .map document no longer cause the autoconverter in order to crash. –pfilter would be to today constantly filter ‘NA’ records. –amount chromosome password output bug repaired. –read-freq now plenty A1 allele rules when they’re missing regarding chief dataset, rather than erroring out in you to situation. –show-tags added to development generate.

Earliest Cochran-Mantel-Haenszel and Breslow-Time evaluating put in development make

4 July: Fixed a few blend pests and this possibly caused investigation in the last couple samples of a feedback otherwise blended fileset as mishandled. ninety leader/beta stimulates, and most several examples was in fact in it, i suggest redoing new mix having a more recent generate. (Extremely merges was basically unchanged, however, most useful safe than just sorry.)

When you have merged filesets made having earlier PLINK step 1

step 1 July: Augment has just delivered (disappointed about this) –data/–gen/–attempt demand-range parsing bug. –indep no more misreports what amount of pruned variations whenever around are thorough multicollinearity. –fst, –homog, and you can –oxford-pheno-label flags additional.

27 June: “–recode oxford” don’t deposits incorrect IDs when found in the same work at while the an example filter. –fill-missing-a2 flag extra. –recode ‘A-transpose’ and you can ‘include-alt’ modifiers extra. “–het small-sample” form added.

20 Summer: Repaired –mendel no chromosome code/segfault insect. –merge-checklist no longer means a resource fileset. –fast-epistasis + –parallel bugfix. –indep-pairphase and QFAM try finished in invention build.

10 Summer: –merge-function step 1 today correctly merges forgotten phone calls which have one nonmissing name. –r/–r2 chromosome boundary dealing with bugfixes. ‘0X’/’0Y’/’0M’ chromosome rules produced by the Oxford tools are now actually acknowledged, and have now backed by –output-chr. –vcf-half-phone call flag put into control management of ‘0/.’ VCF GT thinking, and you will default choices has become ‘error’ mode to force a mindful ent make.

5 June: –ld-snp-number and you will multipass –r/–r2 bugfixes. Nonstandard ‘0/.’ and equivalent VCF GT industry opinions are now processed as the when they didn’t have the fresh at the rear of ‘/.’, as opposed to leading to a great segfault. (Handling of this case is configurable subsequently, listen in.) –linear/–logistic permutation bugfix (permutation success number array wasn’t initialized to all the-zero). –dosage linear regression set in development make.

step three Summer: Gzipper no longer deletes the fresh production file when being asked to append (it was ultimately causing big letter-citation calculations instance –r2 gz to only contain the returns of your history ticket). Repaired –genome double-missing-name addressing bug, and you may an effective –r/–r2 mixed autosomal/nonautosomal data-handling bug. “–serving occur” and you can –write-dosage added to 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” no longer emits areas from the heading range. –blocks presently has an effective ‘no-pheno-req’ modifier hence takes away the excessive phenotype demands. –annotate put in innovation generate.

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