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Thanks, @audy! How are you planning to deal with this? Should I prepare the PR to add Phred decoding to the Python module or wait for you to merge this one? |
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@apcamargo this one is good to merge. I'll merge it now and then you can update #92 if you like. |
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This PR adds Phred decoding functionality to
needletail. The following changes are introduced:qualitymodule:qualitymodule.PhredEncodingenum, representing the type of encoding (Phred+33 or Phred+64).decode_phredfunction, which takes Phred-encoded quality data (&[u8]) and aPhredEncodinginstance, returning the decoded quality scores.errorsmodule:PhredOffsetErrorstruct, representing a Phred-decoding error where the offset (33 or 64, depending on the encoding) exceeds the encoded quality value.SequenceRecord:decode_phredmethod that returns aOptioncontaining 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_phredfunction andrecord::SequenceRecord::decode_phred.The motivation for this PR is to use the added functions in the following PR: #98