5251afff4391b653e4d352ea68fb06d10e99246f
max
  Fri May 31 07:32:51 2024 -0700
adding extra fields to bigPsl docs, refs #17950

diff --git src/hg/htdocs/goldenPath/help/bigPsl.html src/hg/htdocs/goldenPath/help/bigPsl.html
index cbd2d50..9a470f4 100755
--- src/hg/htdocs/goldenPath/help/bigPsl.html
+++ src/hg/htdocs/goldenPath/help/bigPsl.html
@@ -59,33 +59,44 @@
   
     uint    chromSize;		"Size of target chromosome"
   
     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 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>Since bigPsl is just a bigBed file, in addition to these fields, bigPsl
+files can have any number of additional, extra bigBed fields, as
+long as they are defined after the seqType field. 
+See <a href="bigBed.html#Ex3">Example 3</a> of the bigBed documentation page for 
+sample .as and .bed files. These fields can also 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 if you run into difficulty
+using them.</p>
+
 <p>
-Note that the <code>bedToBigBed</code> utility uses a substantial amount of memory: approximately 
-25% more RAM than the uncompressed BED input file.</p>
+The <code>bedToBigBed</code> utility uses a substantial amount of memory: approximately 
+25% more RAM than the uncompressed BED input file. The -maxAllow option to bedToBigBed can be
+used to allow the tool to use more than 16GB of RAM.</p>
 
 <h2>Creating a bigPsl track</h2>
 <p>
 To create a bigPsl track, follow these steps:</p>
 <p> 
 <strong>Step 1.</strong>
 If you already have a PSL file created using BLAT or another tool, skip to <em>Step 2</em>. 
 Otherwise, download the example PSL file <a href="examples/bigPsl.psl"><em>bigPsl.psl</em></a> for 
 the human GRCh38/hg38 assembly. You will also want to download the files 
 <a href="examples/bigPsl.fa"><em>bigPsl.fa</em></a> and 
 <a href="examples/bigPsl.cds"><em>bigPsl.cds</em></a> if you 
 would like to use the alternate options described in <em>Step 4</em>, below.</p>
 <p>
 <strong>Step 2.</strong> 
 Download the <code>bedToBigBed</code> and <code>pslToBigPsl</code> programs from the