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ErasmusMC-CCBC / ProteoDisco

Generates protein variant sequences based on imported mutations from VCF, MAF and additional files to generate a protein-variant database for use in proteogenomics studies
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distanceAssignedCDS and distanceSJtoCDS conflict #6

Closed 1813805349 closed 2 years ago

1813805349 commented 2 years ago

Hi, I'm confused about cryptic CDS. In the first part of the code, cryptic CDS condition(distanceAssignedCDS > maxDistance), but in the latter part of the code, distanceSJtoCDS <=maxDistance.Because distanceSJtoCDS >maxDistance, distanceSJtoCDS must also be greater than maxDistance.So protein sequences cannot be generated. first part image latter part image image

J0bbie commented 2 years ago

You're absolutely right. This must have slipped by during testing.. I've removed the second condition (distanceSJtoCDS <=maxDistance) which indeed would always be the inverse of the prior condition.

Hope this now gives you some interesting results!