Closed thekugelmeister closed 2 years ago
Rather than adding lines that define the missing variables, I would suggest replacing them with the intended final values, just to keep things less verbose.
Ok, good idea. I will add variable definitions to the code block.
Addressed on cleanup branch. Added variable definitions and put as additional lines just so that the database parsing calls are generalizable and user can clearly see how to adapt it to their own code. Will close when merged.
In the documentation for
parse_bam
, the examples under the Return sectionbreak when run as-is, because they reference undefined variables that contain the values for the arguments. Rectifying this is straightforward, as the missing variables clearly map to the argument names, but it would be nice if these commands ran out of the box.