New fix for searchIndex to work within composite tracks in v366

[Brian Lee]

In the recent v366 release we fixed the searchIndex definition to work within composites.  While it has always worked outside of grouped composites, now it will also work for tracks nested within composite groups. 

--Details about searchIndex and searchTrix---

Within hubs you can create search indexes on bigBeds using the bedToBigBed command. Follow example steps here: http://genome.ucsc.edu/goldenPath/help/bigBed.html#Ex3

Here is an example command:

bedToBigBed -as=bedExample2.as -type=bed9+2 -extraIndex=name,geneSymbol bedExample2.bed hg18.chrom.sizes myBigBed2.bb

Once an extraIndex has been built into a bigBed the searchIndex line in a track hub enables that index to be searched:

http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#searchIndex

An example track hub line using searchIndex for a bigBed that had an extraIndex built on the "name" field:

searchIndex name 

The search  mechanism requires an exact match. One can go further and build a TRIX file that has further collection of matching or related terms on an indexed item (for example so that SIR, SIRT, SIRT1, Sir, Sir, Sirt, Sirtuin, would all potentially match with SIRT1). 

Learn about searchTrix here:

http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#searchTrix

http://genome.ucsc.edu/goldenPath/help/trix.html

See an example working hub:

http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubIndexedBigBedSearchable/hub.txt

http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubIndexedBigBedSearchable/hg19/trackDb.txt