Base quality and consensus generation about tracy HOT 7 OPEN

Is this likely to change? As @nriddiford says, it seems a shame to have a 50% chance to incorporate a low quality base when the information is available to make the better call.

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Just to add, I've also been wondering about this!

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@tobiasrausch forgive me for pinging you, but are you intending to respond to this?

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For tracy assemble it's a simple majority vote. If you have, for instance, 3 traces and 2 support a gap - and 1 a nucleotide then the gap - is chosen. Ties are arbitrarily broken and tracy assemble does not take into account qualities at the moment. For the pairwise case, tracy consensus does use the qualities but gaps don't have any to begin with. Therefore, for tracy consensus it depends on whether you use -i or not.

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@tobiasrausch Thanks for the clarification. How about in cases where you have 2 traces (like the image above). Is it just a 50:50 change to incorporate a low quality insertion?

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Indeed, it's a 50:50 chance in theory but in order to make the algorithm deterministic the code currently favours nucleotides over gaps.

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I think tracy consensus in tracy v0.7.5 now properly handles the low-quality vs. high-quality base problem but low-quality insertions vs. gaps is still something I need to work on. Do you have some example traces that you can share with me where you think the insertion is incorrect? Thanks.

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