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Load kmer counts from file #77

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Adamtaranto opened this issue Oct 15, 2024 · 1 comment
Open

Load kmer counts from file #77

Adamtaranto opened this issue Oct 15, 2024 · 1 comment
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enhancement New feature or request

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@Adamtaranto
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oxli is currently slower than other counters for large genomes. Suggest option to bulk load kmer counts from another counter i.e. Jellyfish via text dump.

Would allow users to load pre-calculated counts for use with oxli's python API.

@ctb what do you reckon?

@Adamtaranto Adamtaranto self-assigned this Nov 17, 2024
@Adamtaranto Adamtaranto added the enhancement New feature or request label Nov 17, 2024
@Adamtaranto
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The other option is for users to use the Python API to manually set the counts i.e. kct[kmer] = count.

Only advantage of adding a method to load counts from a dump file is that we could make it multithreaded.

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