cljam.io.fastq — cljam 0.8.3

Functions to read and write the FASTQ format.

casava-1_8-pattern clj

casava-pattern clj

deserialize-casava-1_8-name clj

(deserialize-casava-1_8-name name)

Parse Casava1.8-style name of fastq read.

deserialize-casava-name clj

(deserialize-casava-name name)

Parse Casava-style name of fastq read.

deserialize-name clj

(deserialize-name name)

Try parsing name of fastq read.

FASTQRead clj

read-sequences clj

(read-sequences rdr)

(read-sequences rdr opts)

Returns a lazy sequence of FASTQReads deserialized from given reader.

reader clj

(reader f)

Returns an open cljam.io.fastq.FASTQReader of f. Should be used inside with-open to ensure the reader is properly closed.

serialize-casava-1_8-name clj

(serialize-casava-1_8-name {:keys [instrument run flowcell lane tile x y pair
                                   filtered control index]})

Encode fastq name map to Casava1.8-style string.

serialize-casava-name clj

(serialize-casava-name {:keys [instrument lane tile x y index pair]})

Encode fastq name map to Casava-style string.

serialize-name clj

(serialize-name name)

Try encoding name of fastq read.

write-sequences clj

(write-sequences wtr sequences)

(write-sequences wtr sequences opts)

Write given sequence of reads to a FASTQ file.

writer clj

(writer f)

Returns an open cljam.io.fastq.FASTQWriter of f. Should be used inside with-open to ensure the writer is properly closed.