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/bedgraph.html src/hg/htdocs/goldenPath/help/bedgraph.html
index 83328a5d441..c7e626eb165 100755
--- src/hg/htdocs/goldenPath/help/bedgraph.html
+++ src/hg/htdocs/goldenPath/help/bedgraph.html
@@ -8,70 +8,74 @@
 <h1>BedGraph Track Format</h1>
 <p> 
 The bedGraph format allows display of continuous-valued data in track format. This display type is 
 useful for probability scores and transcriptome data.  This track type is similar to the wiggle 
 (<a href="/goldenPath/help/wiggle.html">WIG</a>) format, but unlike the wiggle format, data exported
 in the bedGraph format are preserved in their original state. This can be seen on export using the
 table browser. For more details on data compression in wiggle tracks see the notes section of the
 wiggle <a href="wiggle.html" target="_blank">track description page</a>. If you have a very large
 data set and you would like to keep it on your own server, you should use the <a href="bigWig.html">
 bigWig</a> data format. In fact, an attempt to load a bedGraph custom track over 50,000,000 lines
 will result in an error message, but can be addressed by turning the bedGraph into a bigWig (see
 <a href="bigWig.html#Ex3">Example 3</a>). Note that bedGraph files cannot easily be converted to
 wiggle files; converting bedGraph to bigWig and using <code>bigWigToWig</code> will return the
 original bedGraph file.</p>
 
+<a id="structure"></a>
 <h2>General Structure</h2>
 <p>
 The bedGraph format is line-oriented. BedGraph data are preceded by a 
 <a href="customTrack.html#TRACK">track definition line</a>, which adds a number of options for 
 controlling the default display of this track.</p> 
 <p> 
 Following the track definition line are the track data in four column BED format:</p>
 
 <pre><code><em>chromA</em>  <em>chromStartA</em>  <em>chromEndA</em>  <em>dataValueA</em>
 <em>chromB</em>  <em>chromStartB</em>  <em>chromEndB</em>  <em>dataValueB</em></code></pre>
 
+<a id="parameters"></a>
 <h3>Parameters for bedGraph track definition lines</h3>
 <p> 
 All options are placed in a single line separated by spaces:</p>
 <pre><code><strong>track type=</strong>bedGraph <strong>name=</strong><em>track_label</em> <strong>description=</strong><em>center_label</em>
     <strong>visibility=</strong><em>display_mode</em> <strong>color=</strong><em>r,g,b</em> <strong>altColor=</strong><em>r,g,b</em>
     <strong>priority=</strong><em>priority</em> <strong>autoScale=</strong><em>on|off</em> <strong>alwaysZero=</strong><em>on|off</em> <strong>gridDefault=</strong><em>on|off</em>
     <strong>maxHeightPixels=</strong><em>max:default:min</em> <strong>graphType=</strong><em>bar|points</em> <strong>viewLimits=</strong><em>lower:upper</em>
     <strong>yLineMark=</strong><em>real-value</em> <strong>yLineOnOff=</strong><em>on|off</em>
     <strong>windowingFunction=</strong><em>maximum|mean|minimum</em> <strong>smoothingWindow=</strong>off|2-16</em></code></pre>
 <p>
 <strong>Note:</strong> if you copy/paste the above example, you must remove the line breaks.</p>
 <p> 
 The track type is REQUIRED, and must be <em>bedGraph</em>:</p>
 <pre><code><strong>type=</strong>bedGraph</code></pre>
 <p> 
 The remaining values are OPTIONAL. The <a href="wiggle.html" target="_blank">wiggle</a> 
 documentation contains details on these options. A functional description of these options can be 
 seen in the <a href="hgWiggleTrackHelp.html" target="_blank">track configuration</a> description. 
 (Custom tracks do not have interactive configuration options.)
 
+<a id="dataValues"></a>
 <h3>Data Values</h3>
 <p>
 BedGraph track data values can be integer or real, positive or negative values. The
 chromosome coordinates are <a href="../../FAQ/FAQtracks.html#tracks1">zero-based, half-open</a>. 
 This means that the first chromosome position is 0, and the last position in a chromosome 
 of length <em>N</em> would be <em>N - 1</em>. The positions listed in the input data must be in 
 numerical order, and only the specified positions will be graphed. bedGraph format has four
 columns of data: <pre><code><em>chrom chromStart chromEnd dataValue</em></code></pre></p> 
 <p>
+<a id="example"></a>
 <h2>Example</h2>
 <p>
 This example specifies 9 separate data points in three tracks on chr19 in the region 49,302,001 to 
 49,304,701. To view this example as a custom track in the Genome Browser, copy the text and paste 
 it into the browser annotation track text box.</p> 
 <pre><code>browser position chr19:49302001-49304701
 browser hide all
 browser pack refGene encodeRegions
 browser full altGraph
 #	300 base wide bar graph, autoScale is on by default == graphing
 #	limits will dynamically change to always show full range of data
 #	in viewing window, priority = 20 positions this as the second graph
 #	Note, zero-relative, half-open coordinate system in use for bedGraph format
 track type=bedGraph name="BedGraph Format" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 priority=20
 chr19 49302000 49302300 -1.0