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Fixes to BLAST functionality and refactoring #39
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Commits on Apr 30, 2024
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Issues addressed here: - Off-target amplicons are now reported as intended in the logs - Off-target amplicons are now always considered last for the final scheme (no penalty is used, but the fact that they had BLAST matches gets recorded) - Amplicon numbering proceeds from 5' to 3' even across pools - In the primer bed file, primers are now ordered according to the amplicon number without taking the pool into account For this, the internal representation of amplicon schemes had to be unified across the different modes and steps of the analysis.
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Commits on May 1, 2024
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This ensures that the best amplicons get the lowest ID numbers in the written scheme.
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Commits on May 2, 2024
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Commits on May 3, 2024
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Optimize amplicon overlap calculations and fix off-by-one errors
... in all interval clculations
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Better use . instead of + for amplicon strand
Amplicons do not really sit on any single strand.
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Commits on May 6, 2024
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Commits on May 7, 2024
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