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/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html index d4d7a979792..a6177957fa6 100755 --- src/hg/htdocs/FAQ/FAQformat.html +++ src/hg/htdocs/FAQ/FAQformat.html @@ -2,68 +2,68 @@ <!--#set var="TITLE" value="Genome Browser FAQ" --> <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Frequently Asked Questions: Data File Formats</h1> <h2>Topics</h2> <h6>General formats</h6> <div class="row"> <!-- Left column --> <div class="col-md-6"> <ul> <li><a href="../goldenPath/help/axt.html">Axt format</a></li> - <li><a href="/goldenPath/help/bam.html">BAM format</a></li> + <li><a name="format5.1"></a><a href="/goldenPath/help/bam.html">BAM format</a></li> <li><a href="#format1">BED format</a></li> <li><a href="#format1.7">BED detail format</a></li> - <li><a href="/goldenPath/help/bedgraph.html">bedGraph format</a></li> + <li><a name="format1.8"></a><a href="/goldenPath/help/bedgraph.html">bedGraph format</a></li> <li><a href="/goldenPath/help/bedMethyl.html">bedMethyl and bigMethyl format</a></li> <li><a href="/goldenPath/help/barChart.html">barChart and bigBarChart format</a></li> - <li><a href="/goldenPath/help/bigBed.html">bigBed format</a></li> + <li><a name="format1.5"></a><a href="/goldenPath/help/bigBed.html">bigBed format</a></li> <li><a href="/goldenPath/help/bigGenePred.html">bigGenePred table format</a></li> - <li><a href="/goldenPath/help/bigPsl.html">bigPsl table format</a></li> + <li><a name="format9.2"></a><a href="/goldenPath/help/bigPsl.html">bigPsl table format</a></li> <li><a href="/goldenPath/help/bigMaf.html">bigMaf table format</a></li> <li><a href="/goldenPath/help/bigChain.html">bigChain table format</a></li> <li><a href="/goldenPath/help/bigNet.html">bigNet table format</a></li> <li><a href="/goldenPath/help/bigNarrowPeak.html">bigNarrowPeak table format</a></li> <li><a href="/goldenPath/help/bigLolly.html">bigLolly table format</a></li> - <li><a href="/goldenPath/help/bigWig.html">bigWig format</a></li> + <li><a name="format6.1"></a><a href="/goldenPath/help/bigWig.html">bigWig format</a></li> <li><a href="../goldenPath/help/chain.html">Chain format</a></li> <li><a href="/goldenPath/help/cram.html">CRAM format</a></li> </ul> </div> <!-- Right column --> <div class="col-md-6"> <ul> <li><a href="/goldenPath/help/decorator.html">Decorator format</a></li> <li><a href="#format9">GenePred table format</a></li> <li><a href="#format3">GFF format</a></li> <li><a href="#format4">GTF format</a></li> <li><a href="#format20">HAL format</a></li> <li><a href="/goldenPath/help/hic.html">Hic format</a></li> <li><a href="/goldenPath/help/heatmap.html">Heatmap format</a></li> <li><a href="/goldenPath/help/interact.html">Interact and bigInteract format</a></li> <li><a href="#format24">Longrange longTabix format</a></li> <li><a href="#format5">MAF format</a></li> <li><a href="#format6.5">Microarray format</a></li> <li><a href="../goldenPath/help/net.html">Net format</a></li> <li><a href="#format10">Personal Genome SNP format</a></li> <li><a href="#format2">PSL format</a></li> - <li><a href="/goldenPath/help/vcf.html">VCF format</a></li> - <li><a href="/goldenPath/help/wiggle.html">WIG format</a></li> + <li><a name="format10.1"></a><a href="/goldenPath/help/vcf.html">VCF format</a></li> + <li><a name="format6"></a><a href="/goldenPath/help/wiggle.html">WIG format</a></li> </ul> </div> </div> <a name="ENCODE"></a> <h6>ENCODE-specific formats</h6> <ul> <li><a href="#format13">ENCODE broadPeak format</a></li> <li><a href="#format14">ENCODE gappedPeak format</a></li> <li><a href="#format12">ENCODE narrowPeak format</a></li> <li><a href="#format16">ENCODE pairedTagAlign format</a></li> <li><a href="#format17">ENCODE peptideMapping format</a></li> <li><a href="#format11">ENCODE RNA elements format</a></li> <li><a href="#format15">ENCODE tagAlign format</a></li> </ul> <h6>Download-only formats</h6>