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/lib/bigPsl.as src/hg/lib/bigPsl.as
index a8c9bdddb2a..7d10b3f36e7 100644
--- src/hg/lib/bigPsl.as
+++ src/hg/lib/bigPsl.as
@@ -2,33 +2,33 @@
 "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 edit list, or empty)"
+    lstring  oSequence;  "Sequence on other side of alignment (or edit list, 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"
     )