This adds support for an optional min-base-quality flag for base-depth that adds a cutoff check for each base. If the base quality for a base is less than the cutoff than the base is recorded as an N instead of as an [A, C, T, G].
Additionally this adds support for bgzipping the output. It does not yet automatically index the bgzipped output.
Lastly, this updates dependencies to latest version and updates the README to stay in sync with the commands options. It also adds a much needed changelog.
This adds support for an optional
min-base-qualityflag forbase-depththat adds a cutoff check for each base. If the base quality for a base is less than the cutoff than the base is recorded as anNinstead of as an[A, C, T, G].Additionally this adds support for bgzipping the output. It does not yet automatically index the bgzipped output.
Lastly, this updates dependencies to latest version and updates the README to stay in sync with the commands options. It also adds a much needed changelog.