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varity.chain
Functions to read, index, and search the chain format. See https://genome.ucsc.edu/goldenPath/help/chain.html for the detail chain format specifications.
Functions to read, index, and search the chain format. See https://genome.ucsc.edu/goldenPath/help/chain.html for the detail chain format specifications.
indexclj
(index chains)Creates chain index for search.
Creates chain index for search.
load-chainclj
(load-chain f)Loads f (e.g. hg19ToHg38.over.chain(.gz)), returning the all contents as a sequence.
Loads f (e.g. hg19ToHg38.over.chain(.gz)), returning the all contents as a sequence.
search-chainsclj
(search-chains chr pos chain-idx)Searches chain entries with chr and pos using the index, returning the results as a sequence. See also varity.chain/index.
Searches chain entries with chr and pos using the index, returning the results as a sequence. See also varity.chain/index.
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