e5759993329b6e609e9ab825991a90283e714088
mspeir
  Wed Sep 9 11:17:57 2026 -0700
Help pages: fix broken internal links and restore anchors people still cite, refs #38062

Three groups of anchor problems on the help and FAQ pages.

Broken internal links, five pages: posters.html listed a 2022 section that
does not exist (no 2022 posters), api.html listed REST and JSON separately
after the two sections were merged, docker.html pointed at a #UsrAcct section
that is not on that page, FAQgenes.html had a capitalized #ncbiRefSeq where
the anchor is #ncbiRefseq, and the genomes.txt settings rows in
trackDbHub.v3.html carried no anchors so its own "genome" link missed.

Retired anchors that are still cited in twenty years of answers on the genome
list. Content moved to its own page and the old anchor was deleted rather than
left behind, so the citations land at the top of the page. Reattached seven
numeric FAQformat anchors to the Topics entry linking to each format's page.
BED, PSL, GFF and GTF were removed from the custom track page in 2012 and
never added back to its list of supported formats; added them with the old
anchors, which fixes customTrack.html and hgTracksHelp.html together since
both include customTrackText.html. Also restored #lines there, and #Session
on hgTrackHubHelp.html and #link4 on FAQlink.html.

Section anchors on six pages that had none, so a support answer can link to
one part of them: bam.html, hic.html, bedgraph.html, ftp.html, net.html and
trackDbIndexBb.html. Skipped quickLiftChain.html, oligoMatch.html and
cutters.html, which are track description fragments included into the details
page rather than standalone pages.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

diff --git src/hg/htdocs/goldenPath/help/trackDbIndexBb.html src/hg/htdocs/goldenPath/help/trackDbIndexBb.html
index 27ea2c519a7..27ad471c7b7 100755
--- src/hg/htdocs/goldenPath/help/trackDbIndexBb.html
+++ src/hg/htdocs/goldenPath/help/trackDbIndexBb.html
@@ -27,30 +27,31 @@
 to be displayed alongside the bigBeds with data.</li>
 </ul>
 
 <p>
 To build the index files, first download the <code>trackDbIndexBb</code> utility. 
 For more information on downloading our command line utilities, see these 
 <a href="http://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads">instructions</a>.</p>
 <p>
 There are three other programs needed to run <code>trackDbIndexBb</code>. Two of them,
 <code>bedToBigBed</code> and <code>bigBedToBed</code>, can be found
 in the same <a href="http://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads">
 downloads directory</a>.
 The final dependency, <b>bedtools</b>, can be found on the <a target="_blank" 
 href="https://bedtools.readthedocs.io/en/latest/">bedtools site</a>.</p>
 
+<a id="parameters"></a>
 <h2>Parameters</h2>
 <p>
 Kent utilities can be run with no parameters to display a usage message. 
 Additionally, <code>trackDbIndexBb</code> can be passed the
 <code>-	h</code> flag to display a more verbose help message.</p>
 <pre>
 ./trackDbIndexBb
 ./trackDbIndexBb -h
 </pre>
 <p> 
 Below is a short description of the parameters:</p>
 <ul>
 <li><b>trackName</b> | The name of the composite containing the bigBed tracks
 to be indexed. Higher-level composite names may be used to build track associations.
 This means that all tracks in the hierarchy <em>below</em> trackName will be searched 
@@ -69,30 +70,31 @@
 Will automatically check current directory and user's path. <code>trackDbIndexBb</code> 
 has three dependencies listed above. Note that bedtools must be downloaded from an 
 external group.</li>
 <li><b>-n --noDelete</b> | (Optional) Keep intermediary multiBed file.</li>
 <li><b>-m --metaDataVar</b> | (Optional) Used only when building track associations. The variable
 designated here will be a trackDb variable which can be used to associate tracks. Default value is
 <em>subGroups</em>, though <em>metaData</em> is also commonly used. See example below for more 
 information.</li>
 <li><b>-s --subGroupRemove</b> | (Optional) Used only when building track associations. In 
 conjunction with <b>--metaDataVar</b>, this variable is used to build track associations. The
 value designated will be excluded as a matching requirement from the trackDb parameter. By 
 default, <em>view</em> is used, though this can change depending on data and organization. 
 See example below for more information.</li>
 </ul>
 
+<a id="example1"></a>
 <h2>Example 1 - Building Index Files</h2>
 <p>
 In this first example, we will build index files for a composite track
 containing 12 bigBed files. Index files hardly improve performance
 on a track with so few files, however, the steps would be the same
 on a larger track.</p>
 <p>
 First, we can take a look at the header stanza for the composite. The complete
 trackDb.ra file is available <a target=_blank" 
 href="/goldenPath/help/examples/trackDbIndexBb/smallExampleTrackDb.ra">here</a>.</p>
 <pre>
 track problematic
 shortLabel Problematic Regions
 longLabel Problematic Regions for NGS or Sanger sequencing or very variable regions
 compositeTrack on
@@ -118,30 +120,31 @@
 <p>
 This will generate two files in the current directory:</p>
 <pre>
 problematic.multiBed.bb
 problematic.multiBedSources.tab
 </pre>
 <p>
 We can then enable the use of these index files for <code>hideEmptySubtracks</code> by
 adding the following two lines to our trackDb.ra file, adjusting the path if needed:</p>
 <pre>
 hideEmptySubtracks off
 hideEmptySubtracksMultiBedUrl problematic.multiBed.bb
 hideEmptySubtracksSourcesUrl problematic.multiBedSources.tab
 </pre>
 
+<a id="example2"></a>
 <h2>Example 2 - Creating Track Associations</h2>
 <p>
 In this longer example, we are looking to build index files with track associations between 
 DNase-seq peak and signal tracks. There are 2 bigBed peak tracks and 4 bigWig signal tracks.
 The complete trackDb for the example can be found <a target=_blank" 
 href="/goldenPath/help/examples/trackDbIndexBb/exampleTrackDb.ra">here</a>.</p> 
 <p>
 Looking at the
 top level stanza, we see that this composite track has two views, one for
 peaks and one for signals. The data are associated with a few different subGroups:</p>
 <pre>
 track uniformDnase
 subGroup4 lab Lab Duke=Duke UW=UW UWDuke=UW-Duke
 subGroup3 view View Peaks=Peaks Signal=Signal
 subGroup2 cellType Cell_Line GM12878=GM12878 H1-hESC=H1-hESC