Add Phred decoding functionality #102
Merged
+117
−4
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This PR adds Phred decoding functionality to
needletail
. The following changes are introduced:quality
module:quality
module.PhredEncoding
enum, representing the type of encoding (Phred+33 or Phred+64).decode_phred
function, which takes Phred-encoded quality data (&[u8]
) and aPhredEncoding
instance, returning the decoded quality scores.errors
module:PhredOffsetError
struct, representing a Phred-decoding error where the offset (33 or 64, depending on the encoding) exceeds the encoded quality value.SequenceRecord
:decode_phred
method that returns aOption
containing the decoded quality scores of FASTQ records. Decoded data is returned as aCow<'a, [u8]>
, which may be coerced toVec<u8>
or&[u8]
.Tests are included for both to the
quality::decode_phred
function andrecord::SequenceRecord::decode_phred
.The motivation for this PR is to use the added functions in the following PR: #98