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/net.html src/hg/htdocs/goldenPath/help/net.html index 9e359055a9a..13a235e7ff4 100755 --- src/hg/htdocs/goldenPath/help/net.html +++ src/hg/htdocs/goldenPath/help/net.html @@ -43,55 +43,58 @@ gap 6515 3 chrU - 5570771 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 7623 1 chrXR_group3a - 1397530 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 7664 1007 chrXR_group3a - 1397008 482 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 fill 7664 382 chrXL_group1e - 8262003 506 id 25608 score 10609 ali 364 qDup 506 type nonSyn tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 7784 4 chrXL_group1e - 8262361 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 7792 3 chrXL_group1e - 8262357 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 7921 2 chrXL_group1e - 8262126 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 7949 9 chrXL_group1e - 8262092 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 8693 1 chrXR_group3a - 1396985 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 fill 9833 1251 chrU - 5562980 1239 id 48675 score 10720 ali 1124 qDup 1094 type top tN 0 qN 0 tR 22 qR 88 tTrf 0 qTrf 0 gap 9966 7 chrU - 5564075 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 10015 3 chrU - 5564030 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 10088 2 chrU - 5563957 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 10101 8 chrU - 5563946 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 </code></pre> +<a id="fields"></a> <h2>Field definitions</h2> <p> The net file consists of 7 fixed fields and a set of optional name/value pair fields. In the descriptions below, <em>target</em> refers to the reference species and <em>query</em> refers to the aligning species.</p> +<a id="fixedFields"></a> <h3>Fixed fields</h3> <ul> <li> <strong><em>Class</em></strong> -- Either <em>fill</em> or <em>gap</em>. Fill refers to a portion of a chain</li> <li> <em><strong>Start in chromosome</em></strong> -- (target species)</li> <li> <em><strong>Size</em></strong> -- target species)</li> <li> <em><strong>Chromosome name</em></strong> -- (query species)</li> <li> <em><strong>Relative orientation</em></strong> -- between target and query species</li> <li> <em><strong>Start in chromosome</em></strong> -- (query species)</li> <li> <em><strong>Size</em></strong> -- (query species)</li> </ul> +<a id="optionalFields"></a> <h3>Optional fields (Name/value pairs)</h3> <ul> <li> <em><strong>id</strong></em> -- ID of associated chain (gapped alignment), if any.</li> <li> <em><strong>score</strong></em> -- Score of associated chain.</li> <li> <em><strong>ali</strong></em> -- Number of bases in alignments in chain.</li> <li> <em><strong>qFar</strong></em> -- For fill that is on the same chromosome as parent, how far fill is from position predicted by parent. This helps determine if a rearrangement is local or if a duplication is tandem.</li> <li> <em><strong>qOver</strong></em> -- Number of bases overlapping with parent gap on query side. Generally, this will be near zero, except for inverts.</li>