4d43b746e730f4cf9df40e70d715e75b33ed6fca mspeir Tue Sep 22 14:43:59 2026 -0700 Explain the bigPsl o-prefixed field names on the help page, refs #37155 The autoSql field comments now name the PSL field each o-prefixed field corresponds to, but nothing on the page said what the o fields are or why they are named after chromosomes when the aligned sequence is usually a transcript or protein. Add a paragraph under the schema block. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/htdocs/goldenPath/help/bigPsl.html src/hg/htdocs/goldenPath/help/bigPsl.html index a4f82cb4f12..0ac1143a608 100755 --- src/hg/htdocs/goldenPath/help/bigPsl.html +++ src/hg/htdocs/goldenPath/help/bigPsl.html @@ -54,30 +54,36 @@ uint oChromSize; "Size of other sequence (PSL qSize)" int[blockCount] oChromStarts;"Start positions in other sequence; relative to oChromStart or oChromStart+oChromSize depending on strand (PSL qStarts)" lstring oSequence; "Sequence on other side of alignment (or empty)" string oCDS; "CDS in NCBI format" uint chromSize; "Size of reference sequence (PSL tSize)" uint match; "Number of bases matched." uint misMatch; "Number of bases that don't match " uint repMatch; "Number of bases that match but are part of repeats " uint nCount; "Number of 'N' bases " uint seqType; "0=empty, 1=nucleotide, 2=amino_acid" ) </code></pre> <p> +The fields that begin with <code>o</code> hold what a PSL file calls the query; the corresponding +PSL field name is given in parentheses above. Despite the <code>Chrom</code> in their names, the +aligned sequence need not be a chromosome, and usually is not one: it is typically a transcript, a +protein, or another query sequence. Alignments between two genomes are normally stored as +<a href="chain.html">chain</a> and <a href="net.html">net</a> files rather than as bigPsl.</p> +<p> The value of the <code>oStrand</code> field indicates whether or not the stored psl data should be reverse-complemented before it is outputted or displayed. This is necessary because the bigPsl file stores reference coordinates on the positive strand, as required by the BED format. The <code>strand</code> field indicates whether the positions in <code>oChromStarts</code> are listed from the chromosome beginning (+) or end (-).</p> <p><b>Additional fields:</b> Since a bigPsl file is a bigBed file, additional fields can be added as bigBed fields. The additional bigBed fields are defined after the seqType field of the bigPsl.as file. See <a href="bigBed.html#Ex3">Example 3</a> of the bigBed Track Format page for an example on how to create a bigBed file with extra (custom) fields. The additional fields can be used for custom <a href="https://genome-blog.gi.ucsc.edu/blog/2022/06/28/track-hub-settings/">mouseOvers</a>, feature filters, and coloring options. Contact us at <A HREF="mailto:genome-www@soe.