| |
Utility functions for phred quality strings.
| (ns cljam.io.sam.util.quality
(:import [java.nio Buffer ByteBuffer CharBuffer]))
|
|
Converts fastq-char to phred-byte.
| (definline fastq-char->phred-byte
[ch]
`(byte (- (int ~ch) 33)))
|
|
Converts phred-byte to fastq-char.
| (definline phred-byte->fastq-char
[b]
`(unchecked-char (unchecked-add (Math/min 93 (Math/max (long ~b) 0)) 33)))
|
|
Converts fastq quality string to phred bytes.
| (defn fastq->phred
^bytes [^String fastq]
(let [b (.getBytes fastq)
in-bb (ByteBuffer/wrap b)
out-bb (ByteBuffer/allocate (alength b))]
(while (.hasRemaining in-bb)
(.put out-bb (fastq-char->phred-byte (.get in-bb))))
(.array out-bb)))
|
|
Converts phred bytes or a byte to fastq quality string or char.
| (defmulti phred->fastq
class)
|
|
Converts phred bytes to fastq quality string.
| (defn phred-bytes->fastq
[^bytes b]
(when-not (nil? b)
(let [bb (ByteBuffer/wrap b)
cb (CharBuffer/allocate (alength b))]
(loop []
(when (.hasRemaining bb)
(.put cb (phred-byte->fastq-char (.get bb)))
(recur)))
(.flip ^Buffer cb)
(.toString cb))))
|
|
|
| (defmethod phred->fastq (class (byte-array nil))
[^bytes b]
(phred-bytes->fastq b))
|
|
|
| (def ^:private ^:const max-phred-score 93)
|
|
|
| (defmethod phred->fastq Integer
[n]
{:pre [(<= 0 n max-phred-score)]}
(phred-byte->fastq-char n))
|
|
| | |