Create a tool to trim BED "overhanging" chromosome coordinates (similar to CleanSam)

Certain tools create datasets with coordinates that start with negative values and/or extend beyond the chromsome end. These are problematic to work with downstream. While text manipulation tools can be used to correct the problem, this is tedious to do and probably only an option for advanced users already familiar with line-command tools.

A tool exists to trim SAM/BAM content. A complimentary tool to clean up interval/bed datasets would be very helpful for users.

If strict BED format was not required, that would be the most flexible implementation (meaning any interval dataset could be input, as long as the start, stop, strand, and database were specified).

Bonuses for usage:
1) Interpret the assigned datatype and trim using that infomation. This includes ignoring headers during processing, but still including the header in the output along with preserving all existing metadata assignments.
2) If any of the required input fields are missing, have the tool form warn the user about what to do (go to "Edit Attibutes" and assign metadata before using). Avoid techincal language and focus on UI "how to" solutions to aid newer/non-technical users.
3) Should the tool fail because of input problems (format), error trap the problem and report it to the user with enough actionable information so that a bug report is not the default path for assistance.
4) Include a help section on the tool form with example expected input formats and details about how to perform metadata assignments.

Thanks for considering!

Start by reviewing the existing CleanSam tool and the repository's conventions for interval or BED tools. Define the input metadata requirements and expected behavior for negative or overlong coordinates, headers, metadata, validation errors, warnings, and help text; the issue is complete when the new tool handles these cases with actionable user guidance.

Written by the indexing model from the issue text.