cljam.io.vcf.util.validator — cljam 0.8.5

check-variant clj

(check-variant validator variant)

Checks if the given variant data is in the format cljam expects, and throws an error if it doesn't conform to the format. Otherwise returns the input variant data. Also, if any validation warning is found, it will be reported to stderr.

check-variants clj

(check-variants validator)

(check-variants validator variants)

Applies check-variant to each element of the given sequence. Returns a lazy sequence of the same elements of the input if there are no invalid variant. The validation is evaluated lazily and throws an exception at the first invalid variant. Returns a transducer if variants is not specified.

make-validator clj

(make-validator meta-info header)

(make-validator {:keys [contig info] format' :format filter' :filter}
                header
                {:keys [file-type ploidy] :or {file-type :vcf ploidy 2}})

Creates a vcf validator that is necessary for variant validation. Takes the following three arguments:

• meta-info: VCF's meta info
• header: VCF's header columns (including mandatory columns)
• options: Validation options The available validation options are:
• :file-type Specify the file type (either of :vcf and :bcf). Defaults to :vcf.
• :ploidy Specify the ploidy of sample genotypes

validate-variant clj

(validate-variant validator variant)

Checks if the given variant data is in the format cljam expects, and returns a validation result map pointing out the problematic portion of data that does not conform to the format. Otherwise returns nil. The validation result map looks like: {:errors {[:chr] ["..."] :warnings {[:pos] ["..."]} :variant { ... variant data ...}}}

validate-variants clj

(validate-variants validator)

(validate-variants validator variants)

Applies validation-variant to each element of the given sequence and collects non-nil validation results into a lazy sequence. Returns a transducer if variants is not specified.