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Introduction

IGB supports search using Lucene indexes.

Use the Lucene indexing code (see tools/Lucene) to create indexes for individual data files or all the data files in a directory. The indexes should be stored in IGBQuickLoad directories along with the data files they are indexing.

Lucene indexes are most useful for enabling search of data files such as EST or probe set alignment files that users don't normally load into memory.

How to index a data file

  1. Build Lucene.zip. Define environment variable IGB_WORKDIR, point it to your copy of checked out genoviz trunk or branch
  2. Unzip Lucene.zip. This will create a directory named Lucene that contains everything you need to index some files.
  3. Go into Lucene/resources and edit the file named index.properties. This file lists fields from each type of file that will be indexed. To find out field names, look at the corresponding SymLoader for that file type.

Example)

To index one file:

To index all files in a directory:

Path must be absolute. Index for files will be in the same directory as the file.

To test and deploy

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