cljam.io.fasta-index.core
The core of FASTA index features.
The core of FASTA index features.
create-indexclj
(create-index in-fa out-fai)Creates a FASTA index file from the sequences.
Creates a FASTA index file from the sequences.
get-headerclj
(get-header fai name')Returns index data and a name [:name, :len, :offset, :line-blen, :line-len]
of the sequence named name.
Returns index data and a name [:name, :len, :offset, :line-blen, :line-len] of the sequence named `name`.
get-headersclj
(get-headers fai)Get offsets of all sequences in the FASTA file. Returns a vector of maps where each element contains the following keys:
:name: The name of the sequence:desc: Always set to "":offset: The file offset value to the sequence
Get offsets of all sequences in the FASTA file. Returns a vector of maps where each element contains the following keys: - `:name`: The name of the sequence - `:desc`: Always set to "" - `:offset`: The file offset value to the sequence
get-indicesclj
(get-indices fai)Get fasta indices with the name of the sequence. Returns a vector of maps where each element contains the following keys:
:name: The name of the sequence:len: Length of the sequence:offset: The file offset value to the sequence:line-blen: The number of bases of each line:line-len: Length of each sequence line (including the newline)
Get fasta indices with the name of the sequence. Returns a vector of maps where each element contains the following keys: - `:name`: The name of the sequence - `:len`: Length of the sequence - `:offset`: The file offset value to the sequence - `:line-blen`: The number of bases of each line - `:line-len`: Length of each sequence line (including the newline)
get-spanclj
(get-span fai name' start end)Calculate byte spans for FASTA file.
Calculate byte spans for FASTA file.
readerclj
(reader f)Returns an open cljam.io.fasta_index.reader.FAIReader of f.
Should be used inside with-open to ensure the reader is properly closed.
Returns an open `cljam.io.fasta_index.reader.FAIReader` of `f`. Should be used inside with-open to ensure the reader is properly closed.
writerclj
(writer f)Returns an open cljam.io.fasta_index.writer.FAIWriter of f.
Should be used inside with-open to ensure the writer is properly closed.
Returns an open `cljam.io.fasta_index.writer.FAIWriter` of `f`. Should be used inside with-open to ensure the writer is properly closed.
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