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Update overlaps.rst
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Julie Sullivan committed Jan 6, 2015
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Expand Up @@ -17,25 +17,23 @@ Install BIOSEG (Postgres versions 9.1 and older only)
Create the index
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You need to create the index on the location table in your production database. This is done simply by adding the `create-location-range-index` post-process step to your `project.xml` file:
You need to create the index on the location table in your production database by adding the `create-location-range-index` post-process step to your `project.xml` file:

.. code-block:: xml
<post-process name="create-location-range-index"/>
If you are using an older version of Postgres, this will create a BIOSEG index. Otherwise it will use a native Postgres index.
If you are using an older version of Postgres, this task will create a BIOSEG index. Otherwise it will use a native Postgres index.

Create the `overlappingFeatures` view
Create the overlappingFeatures view
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Now create the `SequenceFeature.overlappingFeatures` view in the database. This allows you to query for any features that overlap any other types of features in the web interface or query API. Just add the `create-overlap-view` post-process step, it needs to be after `create-location-range-index`.
Create the `SequenceFeature.overlappingFeatures` view in the database. This allows you to query for any features that overlap any other types of features in the web interface or query API. Add the `create-overlap-view` post-process step, which needs to be located **after** `create-location-range-index` in your project XML file.

.. code-block:: xml
<post-process name="create-overlap-view" />
See FlyMine's project.xml for an example of including these steps.

Now any queries on the `overlappingFeatures` collections will use this view and the new index.

.. index:: overlaps, region search, bioseg, genome coordinates, overlappingFeatures, create-overlap-view, create-bioseg-location-index

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