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skoblov-lab / spliceai-reforged

A GPU-friendly implementation of SpliceAI
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Fix tx_starts to match original SpliceAI behavior #4

Closed cfrane closed 1 year ago

cfrane commented 1 year ago

The Reference class was not converting the 0-based transcript start from the annotation file to be 1-based. This caused there to be differences in the model outputs due to the distance from transcript start being off by 1 compared to the original code. After changing this to match the original SpliceAI functionality the transcript start positions need adjusted back to 0-based due to the NCLS find_overlap method being start-exclusive.

edikedik commented 1 year ago

Greetings, @cfrane

Thanks for spotting this.