5709a7858d5c197721be66d5218a79124abadb70 lrnassar Tue Mar 17 08:46:31 2026 -0700 Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254 diff --git src/hg/htdocs/goldenPath/help/cram.html src/hg/htdocs/goldenPath/help/cram.html index 0190be4e56c..efc6227700c 100755 --- src/hg/htdocs/goldenPath/help/cram.html +++ src/hg/htdocs/goldenPath/help/cram.html @@ -59,31 +59,31 @@ management page, click submit and view it in the Browser. The track name will then be the name of the file. If you want to configure the track name and descriptions, you will need to create a track line, as shown in the above example. Learn more about track line options and configuring custom tracks <a href="hgTracksHelp.html#TRACK" target="_blank">here</a>.</p> <p> Here is an example URL to a CRAM file from the 1000 Genomes Project that can be pasted directly into the <a href="/cgi-bin/hgCustom?db=hg19" target="_blank">Custom Tracks</a> page:</p> <pre><code>ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/exome_alignment/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram </code></pre> <p> You can see by adding the above link the Browser automatically assigns the <code>type=bam</code> and the <code>track name=HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam</code> to the created track to browse.</p> <p> Clicking the following image will load a CRAM file from the 1000 Genomes Project. <a href="../../cgi-bin/hgTracks?db=hg19&position=chr21%3A33031597-33041570&hgct_customText=track%20type=bam%20name=%22CRAM Example%22%20description=%22A%201000%20Genomes%20CRAM%20file%22%20visibility=full%20bigDataUrl=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00139/exome_alignment/HG00139.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.cram%20doWiggle=1" -target="_blank"><img src="../../images/session.hg19.cramExample.png"></a></p> +target="_blank"><img alt="Browser session displaying a 1000 Genomes CRAM file with read alignment density" src="../../images/session.hg19.cramExample.png"></a></p> <p> This CRAM display takes advantage of using the new "density graph" feature where the bam.cram reads are displayed as a bar graph by checking the box next to "Display data as a density graph" on the Custom Track Settings page.</p> <h2>Example #3</h2> <p> The CRAM format is also supported in track hubs. Below is an example trackDb.txt stanza that would display a CRAM files from the 1000 Genomes Project. To learn more about using Track Hubs see the <a href="hgTrackHubHelp.html" target="_blank">User Guide</a> and associated Quick Start Guides to building hubs. Note that <code>type bam</code> is used to display CRAM files in hubs, just as <code>type bam</code> is used in custom CRAM tracks.</p> <pre><code>track cram61 type bam shortLabel HG00361