cljam.io.sam.util.validator — cljam 0.8.5

check-alignment clj

(check-alignment validator alignment)

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

check-alignments clj

(check-alignments validator)

(check-alignments validator alignments)

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

make-validator clj

(make-validator header)

(make-validator header {:keys [file-type] :or {file-type :sam}})

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

• header: SAM's header columns (including mandatory columns)
• options: Validation options The available validation options are:
• :file-type Specify the file type (either of :sam and :bam). Defaults to :sam

validate-alignment clj

(validate-alignment validator alignment)

Checks if the given alignments 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] ["..."]} alignment { ... alignment data ...}}}

validate-alignments clj

(validate-alignments validator)

(validate-alignments validator alignments)

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