Recipes
=======

This section provides practical examples and patterns for common genomic analysis tasks
using GIQL. Each recipe focuses on a specific use case with ready-to-use query patterns.

Recipe Categories
-----------------

:doc:`intersect`
   Finding overlapping features, filtering by overlap, counting overlaps,
   strand-specific operations, and join patterns.

:doc:`distance`
   Calculating distances between features, finding nearest neighbors,
   distance-constrained searches, and directional queries.

:doc:`clustering`
   Clustering overlapping intervals, distance-based clustering,
   merging intervals, and aggregating cluster statistics.

:doc:`disjoin`
   Splitting intervals at breakpoints, partitioning a set into
   non-overlapping segments, and re-tiling features against a reference grid.

:doc:`advanced`
   Multi-range matching, complex filtering with joins, aggregate statistics,
   window expansions, and multi-table queries.

Coming from Bedtools?
---------------------

If you're familiar with bedtools and want to replicate specific commands in GIQL,
see the :doc:`bedtools-migration` guide for a complete mapping of bedtools
operations to GIQL equivalents.