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cljam.io.vcf.util.normalize
make-splitterclj
(make-splitter {:keys [info format]} header)Returns a function that splits a multiallelic variant into a sequence of biallelic variants.
Returns a function that splits a multiallelic variant into a sequence of biallelic variants.
normalizeclj
(normalize ref-reader meta-info header)(normalize ref-reader meta-info header variants)Splits multiallelic variants and realigns all alleles. Returns a lazy
sequence of normalized variants. Note that the result may be unsorted due to
the realignment. Returns a transducer when no variant is provided. The
transducer does not guarantee thread safety of ref-reader.
Splits multiallelic variants and realigns all alleles. Returns a lazy sequence of normalized variants. Note that the result may be unsorted due to the realignment. Returns a transducer when no variant is provided. The transducer does not guarantee thread safety of `ref-reader`.
realignclj
(realign seq-reader variant)(realign seq-reader
{:keys [ref alt] :as variant}
{:keys [window] :or {window 100}})Left-align and trim REF/ALT alleles.
Left-align and trim REF/ALT alleles.
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