cljam.io.fasta.reader — cljam 0.8.0

create-ba clj

(create-ba buffer)

load-headers clj

(load-headers rdr)

RandomAccessor clj protocol

get-file-pointer clj

(get-file-pointer this)

read-buffer clj

(read-buffer this start end)

read-line clj

(read-line this)

seek clj

(seek this pos)

read clj

(read rdr)

Reads FASTA sequence data, returning its information as a lazy sequence.

read-sequence clj

(read-sequence rdr name start end {:keys [mask?]})

read-sequences clj

(read-sequences rdr)

Reads sequences by line, returning the line-separated sequences as lazy sequence.

reset clj

(reset rdr)

sequential-read-byte-array clj

(sequential-read-byte-array stream page-size seq-buf-size)

Returns list of maps containing sequence as byte-array. Bases ACGTN are encoded as 1-5.

sequential-read-string clj

(sequential-read-string stream page-size seq-buf-size {:keys [mask?]})

Returns list of maps containing sequence as upper-case string.