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This tweaks the PB CCS profile (HiFi) parameters to no longer restrict the maximum quality value, as requested by users as some software explicitly searches for Q93. The old parameters can be explicitly set if desired.
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A major speed increase to the low-complexity mask functionality, particularly important for long read technologies.
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Add a -k/-K options to keep (preserve) specific quality values. For example
-k 93will preserve maximum Sequel II HiFi quality.-kpreserves these scores when deemed appropriate - such as having discrepant calls in the pileup - while-Kpreserves them for all bases.