This PR adds a new flag to artic minion, allowing the user to choose whether or not to use flag -A (--auto_max_cov) when running longshot.
By default, the flag -A is used, so that current behavior remains unchanged upon updating. When setting --no-auto_max_cov, the call to longshot is made without flag -A.
This PR adds a new flag to
artic minion, allowing the user to choose whether or not to use flag-A(--auto_max_cov) when runninglongshot. By default, the flag-Ais used, so that current behavior remains unchanged upon updating. When setting--no-auto_max_cov, the call tolongshotis made without flag-A.This change closes issue #91.