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/inc/bigTransMap.h src/hg/inc/bigTransMap.h
index 40305446aa8..39e18ee7768 100644
--- src/hg/inc/bigTransMap.h
+++ src/hg/inc/bigTransMap.h
@@ -13,38 +13,38 @@
 /* bigPsl derived pairwise alignment with additional information */
     {
     struct bigTransMap *next;  /* Next in singly linked list. */
     char *chrom;	/* Reference sequence chromosome or scaffold */
     unsigned chromStart;	/* Start position in chromosome */
     unsigned chromEnd;	/* End position in chromosome */
     char *name;	/* alignment Id */
     unsigned score;	/* Score (0-1000), faction identity * 1000 */
     char strand[2];	/* + or - indicates whether the query aligns to the + or - strand on the reference */
     unsigned thickStart;	/* Start of where display should be thick (start codon) */
     unsigned thickEnd;	/* End of where display should be thick (stop codon) */
     unsigned reserved;	/* RGB value (use R,G,B string in input file) */
     int blockCount;	/* Number of blocks */
     int *blockSizes;	/* Comma separated list of block sizes */
     int *chromStarts;	/* Start positions relative to chromStart */
-    unsigned oChromStart;	/* Start position in other chromosome */
-    unsigned oChromEnd;	/* End position in other chromosome */
+    unsigned oChromStart;	/* Start position in other sequence (PSL qStart) */
+    unsigned oChromEnd;	/* End position in other sequence (PSL qEnd) */
     char oStrand[2];	/* + or -, - means that psl was reversed into BED-compatible coordinates */
-    unsigned oChromSize;	/* Size of other chromosome. */
-    int *oChromStarts;	/* Start positions relative to oChromStart or from oChromStart+oChromSize depending on strand */
-    char *oSequence;	/* Sequence on other chrom (or edit list, or empty) */
+    unsigned oChromSize;	/* Size of other sequence (PSL qSize) */
+    int *oChromStarts;	/* Start positions in other sequence; relative to oChromStart or oChromStart+oChromSize depending on strand (PSL qStarts) */
+    char *oSequence;	/* Sequence on other side of alignment (or edit list, or empty) */
     char *oCDS;	/* CDS in NCBI format */
-    unsigned chromSize;	/* Size of target chromosome */
+    unsigned chromSize;	/* Size of reference sequence (PSL tSize) */
     unsigned match;	/* Number of bases matched. */
     unsigned misMatch;	/*  Number of bases that don't match  */
     unsigned repMatch;	/*  Number of bases that match but are part of repeats  */
     unsigned nCount;	/*  Number of 'N' bases  */
     unsigned seqType;	/* 0=empty, 1=nucleotide, 2=amino_acid */
     char *srcDb;	/* source database */
     char *srcTransId;	/* source transcript id */
     char *srcChrom;	/* source chromosome */
     unsigned srcChromStart;	/* start position in source chromosome */
     unsigned srcChromEnd;	/* end position in source chromosome */
     unsigned srcIdent;	/* source score (fraction identity * 1000) */
     unsigned srcAligned;	/* fraction of source transcript aligned (fraction aligned * 1000) */
     char *geneName;	/* gene name */
     char *geneId;	/* gene id */
     char *geneType;	/* gene type */