SQLite - Are there alternatives to rtree for indexing lines on an axis?

I'm trying to make开发者_StackOverflow社区 a database of positions with a start and stop: basically lines on a 1D axis. I want to efficiently query all positions that overlap a given interval. In a traditional table, the query would require two inequalities, so it cannot be indexed. You can also use an R-Tree index, but they seem designed for multidimensional range queries. Is there a more efficient way to store lines on an axis?

If anybody curious, the database is to store genome intervals. Here's an example table:

CREATE TABLE lines (id INTEGER PRIMARY KEY, start INTEGER, stop INTEGER);

The basic way to do this is:

SELECT * FROM lines WHERE start <= <end of interval> AND stop >= <start of interval>;

Again, that's really slow and can't be indexed. The R-Tree would work like this:

CREATE VIRTUAL TABLE lines_index USING RTREE (id, start, stop);
SELECT * from lines_index WHERE start <= <end of interval> AND stop >= <start of interval>;

R-Trees aren't ideal for our implementation, so I'm wondering if there are any alternatives...

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First of all, allthough you can't fully index it you could index by just the start interval. If 90% of the intervals have start=stop, that should make a big improvement. The only slowdown would be with very long intervals.