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Public Vars

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.

index

(index chains)
Creates chain index for search.
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load-chain

(load-chain f)
Loads f (e.g. hg19ToHg38.over.chain(.gz)), returning the all contents as a
sequence.
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search-chains

(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.
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search-containing-chains

(search-containing-chains chr start end chain-idx)
Calculates a list of chains that contain the given interval.
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search-overlap-blocks

(search-overlap-blocks start end blocks-idx)
Calculates a list of blocks that overlap the given interval.
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