Functions to read and write the FASTQ format.
Functions to read and write the FASTQ format.
(deserialize-casava-1_8-name name)
Parses Casava1.8-style name of fastq read.
Parses Casava1.8-style name of fastq read.
(deserialize-casava-name name)
Parses Casava-style name of fastq read.
Parses Casava-style name of fastq read.
(deserialize-name name)
Tries parsing name of fastq read.
Tries parsing name of fastq read.
(read-sequences rdr)
(read-sequences rdr opts)
Returns a lazy sequence of FASTQReads deserialized from given reader.
Returns a lazy sequence of FASTQReads deserialized from given reader.
(reader f)
Returns an open cljam.io.fastq.FASTQReader of f. Should be used inside with-open to ensure the reader is properly closed.
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 {:keys [instrument run flowcell lane tile x y pair
filtered control index]})
Encodes fastq name map to Casava1.8-style string.
Encodes fastq name map to Casava1.8-style string.
(serialize-casava-name {:keys [instrument lane tile x y index pair]})
Encodes fastq name map to Casava-style string.
Encodes fastq name map to Casava-style string.
(serialize-name name)
Tries encoding name of fastq read.
Tries encoding name of fastq read.
(write-sequences wtr sequences)
(write-sequences wtr sequences opts)
Writes given sequence of reads to a FASTQ file.
Writes given sequence of reads to a FASTQ file.
(writer f)
Returns an open cljam.io.fastq.FASTQWriter of f. Should be used inside with-open to ensure the writer is properly closed.
Returns an open cljam.io.fastq.FASTQWriter of f. Should be used inside with-open to ensure the writer is properly closed.
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