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varity.vcf-lift
liftover-variantclj
(liftover-variant target-seq-reader indexed-chain variant)Lifts over a variant to another coordinate. Returns a converted and
realigned variant if succeeded to lift over, otherwise nil.
indexed-chain supplies conversions between sequences and must be indexed by
varity.chain/index. target-seq-reader is a reader instance of the target
sequence that the variant coordinate is converted to.
Lifts over a `variant` to another coordinate. Returns a converted and realigned variant if succeeded to lift over, otherwise nil. `indexed-chain` supplies conversions between sequences and must be indexed by `varity.chain/index`. `target-seq-reader` is a reader instance of the target sequence that the variant coordinate is converted to.
liftover-variant*clj
(liftover-variant* indexed-chain {:keys [chr pos ref info] :as variant})liftover-variant without checking reference sequence and realignment.
`liftover-variant` without checking reference sequence and realignment.
liftover-variantsclj
(liftover-variants seq-reader indexed-chains variants)Lifts over variants data from chains applied chain/index and seq-reader. Variants that succeed in liftover will be put in :success, and those that failed will be put in :failure.
Lifts over variants data from chains applied chain/index and seq-reader. Variants that succeed in liftover will be put in :success, and those that failed will be put in :failure.
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