90c7c79830fcf633543d0fdb16fdbc21f1ae6e6f
max
  Fri Apr 21 02:42:26 2023 -0700
#Preview2 week - bugs introduced now will need a build patch to fix
various doc fixes related to bigDataIndex, no redmine, email and galaxy ticket with Jennifer Jackson, see https://help.galaxyproject.org/t/send-files-from-galaxy-to-ucscs-eu-mirror/9921/3

diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html
index 5efba19..1d364cf 100755
--- src/hg/htdocs/goldenPath/help/customTrackText.html
+++ src/hg/htdocs/goldenPath/help/customTrackText.html
@@ -637,30 +637,38 @@
   string this will be substituted with the item name. There is no default for this attribute.</li> 
   <li>
   <strong>htmlUrl=<<em>external_url</em>></strong> - Defines a URL for an HTML description page to 
   be displayed with this track. There is no default for this attribute.  A template for a standard 
   format HTML track description is <a class="change" target="_blank" 
   href="http://genome.ucsc.edu/goldenPath/help/ct_description.txt">here</a>.</li> 
   <li>
   <strong>bigDataUrl=<<em>external_url</em>></strong> - Defines a URL to the data file for 
   <a href="../help/bam.html" target="_blank">BAM</a>,
   <a href="../help/cram.html" target="_blank">CRAM</a>,
   <a href="../help/bigBed.html" target="_blank">bigBed</a>,
   <a href="../help/bigWig.html" target="_blank">bigWig</a> or
   <a href="../help/vcf.html" target="_blank">VCF</a> tracks. This is a required attribute for those 
   track types. There is no default for this attribute.</li>
   <li>
+  <strong>bigDataIndex=<<em>external_url</em>></strong> - Optional. The URL of the BAI/TBI index file for 
+  <a href="../help/bam.html" target="_blank">BAM</a> and
+  <a href="../help/cram.html" target="_blank">CRAM</a> files. By default, these index files are assumed
+  to be at the same URL as the data file, but with the extension .bai. For example, if the data file is
+  https://genome.gov/genome.bam, the index file by default must be at https://genome.gov/genome.bam.bai.
+  If that is not the case, the bigDataIndex option must be used to point to the index file.
+  </li>
+  <li>
   <strong>doWiggle=<<em>on</em>></strong> - The doWiggle setting enables BAM custom tracks
   to be displayed as bar graphs where the height is proportional to the number of reads mapped
   to each genomic position. This display is described as a density graph and is best viewed with
   the track set to full and scaling set to auto-scale. See the Track Database Definition
   <a href="../help/trackDb/trackDbHub.html#doWiggle" target="_blank">doWiggle entry</a>
   for more information about the use in hubs and the
   <a href="../help/hgBamTrackHelp" target="_blank">configuring BAM tracks</a> and the
   <a href="../help/hgWiggleTrackHelp.html" target="_blank">configuring graph-based tracks</a>
   help pages to learn how to further change the display.</li>
 </ul>
 <p>
 Here is an example of a properly formatted track line using the bigBed format, with accompanying 
 browser line:</p>
 <pre><code>browser position chr21:33,031,597-33,041,570
 track type=bigBed name="bigBed Example One" description="A bigBed file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb</code></pre>