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Add insertion sequence to nuc.csv and amino.csv #768

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CBeelen opened this issue Nov 10, 2021 · 0 comments
Open

Add insertion sequence to nuc.csv and amino.csv #768

CBeelen opened this issue Nov 10, 2021 · 0 comments
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@CBeelen
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CBeelen commented Nov 10, 2021

Currently, insertions in the consensus relative to the reference are reported in nuc.csv and amino.csv as counts in the insertions column, but the actual insertion sequence is not included. Users have reported back that it would be useful to have access to the sequence of the consensus insertion in these files as well.

Add the consensus insertion sequence in nuc.csv and amino.csv, with their respective consensus coordinates and blank reference coordinates - this is equivalent to how deletions are treated, with blank consensus positions. Think about how to use the insertions column in these cases - should it report the total insertions count for the insertion positions only (in contrast to reporting insertions after a certain position right now)?

This could be implemented in the same way that insertions are handled for the stitched consensus, by adding them into the region nucleotides and aminos with non-integer positions, so they end up between the correct reference positions.

@CBeelen CBeelen added this to the 7.17 milestone May 25, 2023
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