198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/makeDb/trackDb/ebola/gireIntraHost.html src/hg/makeDb/trackDb/ebola/gireIntraHost.html index 8ca34467dee..721b97de4bd 100644 --- src/hg/makeDb/trackDb/ebola/gireIntraHost.html +++ src/hg/makeDb/trackDb/ebola/gireIntraHost.html @@ -1,45 +1,45 @@ <H2>Description</H2> <p> This track represents intrahost variants for a subset of the 78 Sierra Leone EVD patients described in Gire <em>et al</em>., 2014. For a subset of these 78 patients, researchers took multiple blood samples from each patient at various time points, then isolated and sequenced the Ebola virus from -each sample. This allowed them to to track the mutation and evolution of the virus within a single +each sample. This allowed them to track the mutation and evolution of the virus within a single patient or host. </p> <H2>Display Conventions</H2> <p> In "dense" mode, a vertical line is drawn at the position of each variant. In "full" mode, in addition to the vertical line, a label to the left shows the reference allele first and variant alleles below (<span style='color:red;'>A = red</span>, <span style='color:blue;'>C = blue</span>, <span style='color:green;'>G = green</span>, <span style='color:magenta;'>T = magenta</span>, Indels = black). Hovering the pointer over any variant will prompt the display of the occurrences numbers for each allele in Gire <em>et al</em>., 2014. Clicking on any variant will result in full details of that variant being displayed.</p> <p> By default, in "pack" mode, the display shows a clustering of haplotypes in the viewed range, sorted by similarity of alleles weighted by proximity to a central variant. The clustering view can highlight local patterns of linkage.</p> <p> Each variant is a vertical bar with white (invisible) representing the reference allele and black representing the non-reference allele(s). Tick marks are drawn at the top and bottom of each variant's vertical bar to make the bar more visible when most alleles are reference alleles. The vertical bar for the central variant used in clustering is outlined in purple. In order to avoid long compute times, the range of alleles used in clustering may be limited; alleles used in clustering have purple tick marks at the top and bottom.</p> <p> The clustering tree is displayed to the left of the main image. It does not represent relatedness of individuals; it simply shows the arrangement of local haplotypes by similarity. When a rightmost branch is purple, it means that all haplotypes in that branch are identical, at least within the range of variants used in clustering. </p> <!--#insert file="gireMethods.html"--> <!--#insert file="gireReferences.html"-->