ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029
braney
  Wed Apr 8 14:57:47 2026 -0700
Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

diff --git src/hg/htdocs/goldenPath/help/bigPsl.html src/hg/htdocs/goldenPath/help/bigPsl.html
index 17f200235ef..a4f82cb4f12 100755
--- src/hg/htdocs/goldenPath/help/bigPsl.html
+++ src/hg/htdocs/goldenPath/help/bigPsl.html
@@ -36,40 +36,40 @@
 "bigPsl pairwise alignment"  
     ( 
     string chrom;       	"Reference sequence chromosome or scaffold"
     uint   chromStart;  	"Start position in chromosome"
     uint   chromEnd;    	"End position in chromosome"
     string name;        	"Name or ID of item, ideally both human readable and unique"
     uint score;         	"Score (0-1000)"
     char[1] strand;     	"+ or - indicates whether the query aligns to the + or - strand on the reference"
     uint thickStart;    	"Start of where display should be thick (start codon)"
     uint thickEnd;      	"End of where display should be thick (stop codon)"
     uint reserved;       	"RGB value (use R,G,B string in input file)"
     int blockCount;     	"Number of blocks"
     int[blockCount] blockSizes; "Comma separated list of block sizes"
     int[blockCount] chromStarts;"Start positions relative to chromStart"
 
-    uint    oChromStart;	"Start position in other chromosome"
-    uint    oChromEnd;  	"End position in other chromosome"
+    uint    oChromStart;	"Start position in other sequence (PSL qStart)"
+    uint    oChromEnd;  	"End position in other sequence (PSL qEnd)"
     char[1] oStrand;    	"+ or -, - means that psl was reversed into BED-compatible coordinates"
-    uint    oChromSize; 	"Size of other chromosome."
-    int[blockCount] oChromStarts;"Start positions relative to oChromStart or from oChromStart+oChromSize depending on strand"
+    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 chrom (or empty)"
+    lstring  oSequence;  	"Sequence on other side of alignment (or empty)"
     string   oCDS;       	"CDS in NCBI format"
 
-    uint    chromSize;		"Size of target chromosome"
+    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 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>