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cljam.io.twobit.reader
clone-readerclj
(clone-reader rdr)Clones .2bit reader sharing persistent objects.
Clones .2bit reader sharing persistent objects.
mask!clj
(mask! cb masks start end)Mask regions of given charbuffer.
Mask regions of given charbuffer.
read-all-sequencesclj
(read-all-sequences rdr)(read-all-sequences rdr option)Reads all sequences in file.
Reads all sequences in file.
read-indicesclj
(read-indices rdr)Reads metadata of indexed sequences. Forces loading all indices.
Reads metadata of indexed sequences. Forces loading all indices.
read-seq-summariesclj
(read-seq-summaries rdr)Reads summaries of sequences in this 2bit file.
Reads summaries of sequences in this 2bit file.
read-sequenceclj
(read-sequence rdr region)(read-sequence rdr {:keys [chr start end]} {:keys [mask?] :or {mask? false}})Reads sequence at the given region from reader. Pass {:mask? true} to enable masking of sequence.
Reads sequence at the given region from reader.
Pass {:mask? true} to enable masking of sequence.replace-ambs!clj
(replace-ambs! cb ambs start end)Replace regions of charbuffer with Ns.
Replace regions of charbuffer with Ns.
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