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Indel discount feature #115

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Indel discount feature #115

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@bwlang bwlang commented Jan 7, 2022

fixes issue #114

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bwlang commented Jan 7, 2022

This hardcoded discount is a proof of concept... it produces the desired consensus sequence (discount_ivar.fa) but needs more work to figure out how to get an option into the user interface and to confirm that it does not produce unwanted indels elsewhere.

(seq) ➜  data git:(indel_discount) ✗ cut -c 22180-22240 std_ivar.fa

GCACACGCCTATTATAGTGCGTNNNNNNNNNGATCTCCCTCAGGGTTTTTCGGCTTTAGAA
(seq) ➜  data git:(indel_discount) ✗ cut -c 22180-22240 discount_ivar.fa

GCACACGCCTATTATAGTGCGTGAGCCAGAAGATCTCCCTCAGGGTTTTTCGGCTTTAGAA```

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