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cljam.io.fasta.core
clone-readerclj
(clone-reader rdr)Clones fasta reader sharing persistent objects.
Clones fasta reader sharing persistent objects.
readclj
(read rdr)Returns a lazy sequence of maps representing each sequence in FASTA.
Returns a lazy sequence of maps representing each sequence in FASTA.
read-headersclj
(read-headers rdr)Returns fasta headers(offset, name and desc).
Returns fasta headers(offset, name and desc).
read-seq-summariesclj
(read-seq-summaries rdr)Reads summaries of sequences in this FASTA file.
Reads summaries of sequences in this FASTA file.
read-sequenceclj
(read-sequence rdr {:keys [chr start end]} opts)Reads the specified range of sequence. Start and end can be null.
Reads the specified range of sequence. Start and end can be null.
read-sequencesclj
(read-sequences rdr)Reads sequences by line, returning the line-separated sequences as lazy sequence.
Reads sequences by line, returning the line-separated sequences as lazy sequence.
readerclj
(reader f)Makes FastaReader from the File.
Makes FastaReader from the File.
resetclj
(reset rdr)Resets the file pointer of rdr.
Resets the file pointer of rdr.
sequential-readclj
(sequential-read rdr)(sequential-read rdr opts)Returns a list of maps containing sequence as upper-case string.
Returns a list of maps containing sequence as upper-case string.
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