Provide a way to search for features that only overlap the data start or stop

[hepcat72]

If someone wants to search for features that are upstream of a pair of data coordinates, but will tolerate a degree of overlap, there's no way to specify that currently. You can only specify upstream and overlap, which includes features that overlap only the stop coordinate.

You CAN sort-of specify that you want to only consider a feature's start coordinate by specifying the start and stop as the same column in the data, but that doesn't help when start/stop are not logically ordered and you need the strand to infer which one is the start, therefor options like '--search-overlap-start' and '--search-overlap-stop' could overcome that and allow start and stop to both be specified. You might even want to ensure that the other end does NOT overlap, like --search-overlap-start-only... whereas --search-overlap-start would not care if the stop also overlaps. Note, I'm not even sure if the code currently accounts for un-ordered start/stop columns.

By the same token, you might want to specify whether the start/stop of a feature should overlap or not.

Nor is a degree of overlap capable of being specified.

It might be a good idea to allow -r to use negative values as the amount of allowed overlap. Currently, a negative value means no limit to the search range, but I could change that to simply un-supplied/undefined. Note, I will have to handle the situation where the negative value results in a coordinate outside of the data coordinates (e.g. if -r -10 and start/stop = 5/10, then the location where it would start searching in the case of --search-upstream would be 15, i.e. 'downstream'). it might even be desirable to specify the degree of overlap allowed via percentage/ratio.

All this would also apply to other search types such as downstream, left, right, etc..