Handle MT values as NaN to avoid string comparison

LiuzLab / AI_MARRVEL

AI-MARRVEL (AIM) is an AI system for rare genetic disorder diagnosis

GNU General Public License v3.0

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Handle MT values as NaN to avoid string comparison #32

Closed jylee-bcm closed 1 month ago

jylee-bcm commented 2 months ago

This is main branch version for one of optimization works done in the nextflow branch.

It reduces the running time of 2.5 minutes for demo.vcf.gz on elpaso server, this running time may differ by your machine. For more details, please refer the link to https://github.com/hyunhwan-bcm/AI_MARRVEL/pull/1

This change ensures that MT (Mitochondria) values are treated as -1 to mean NaN (Not a Number), improving the speed by eliminating string comparisons.

hyunhwan-bcm commented 1 month ago

will be merged with nextflow_conversion