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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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Unpolished bases as lower case #117

Closed mrvollger closed 2 years ago

mrvollger commented 5 years ago

Just a suggesting an enhancement.

When using -u it would be nice if unpolished bases were lowercase.

Best, Mitchell

rvaser commented 5 years ago

Hi Mitchell, are you suggesting that the bases of unpolished sequences (sequences outputted when using -u) are all lowercase or would you like to have lowercase bases in both polished and unpolished sequences?

Sorry for the late response! Best regards, Robert

mrvollger commented 5 years ago

Hi Robert,

I was suggesting that when -u is used that unpolished bases are lowercase, and polished bases are uppercase, or perhaps a new flag with this behavior. If it helps convince you this is the defualt now used by the PacBio polishers https://github.com/PacificBiosciences/GenomicConsensus/blob/develop/doc/FAQ.rst#what-does-it-mean-that-quiver-consensus-is-de-novo. It is not a big deal, but it is helpful in downstream analysis to be able to make separate quality scores for polished and unpolished bases, and lower/upper case makes that distinction easy.

No worries.

Best, Mitchell