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
@@ -1,98 +1,98 @@
 /* bigTransMap.h was originally generated by the autoSql program, which also 
  * generated bigTransMap.c and bigTransMap.sql.  This header links the database and
  * the RAM representation of objects. */
 
 #ifndef BIGTRANSMAP_H
 #define BIGTRANSMAP_H
 
 #define BIGTRANSMAP_NUM_COLS 40
 
 extern char *bigTransMapCommaSepFieldNames;
 
 struct bigTransMap
 /* 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 */
     char *transcriptType;	/* transcript type */
     char *chainType;	/* type of chains used for mapping */
     char *commonName;	/* common name */
     char *scientificName;	/* scientific name */
     char *orgAbbrev;	/* organism abbreviation */
     };
 
 struct bigTransMap *bigTransMapLoad(char **row);
 /* Load a bigTransMap from row fetched with select * from bigTransMap
  * from database.  Dispose of this with bigTransMapFree(). */
 
 struct bigTransMap *bigTransMapLoadAll(char *fileName);
 /* Load all bigTransMap from whitespace-separated file.
  * Dispose of this with bigTransMapFreeList(). */
 
 struct bigTransMap *bigTransMapLoadAllByChar(char *fileName, char chopper);
 /* Load all bigTransMap from chopper separated file.
  * Dispose of this with bigTransMapFreeList(). */
 
 #define bigTransMapLoadAllByTab(a) bigTransMapLoadAllByChar(a, '\t');
 /* Load all bigTransMap from tab separated file.
  * Dispose of this with bigTransMapFreeList(). */
 
 struct bigTransMap *bigTransMapCommaIn(char **pS, struct bigTransMap *ret);
 /* Create a bigTransMap out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new bigTransMap */
 
 void bigTransMapFree(struct bigTransMap **pEl);
 /* Free a single dynamically allocated bigTransMap such as created
  * with bigTransMapLoad(). */
 
 void bigTransMapFreeList(struct bigTransMap **pList);
 /* Free a list of dynamically allocated bigTransMap's */
 
 void bigTransMapOutput(struct bigTransMap *el, FILE *f, char sep, char lastSep);
 /* Print out bigTransMap.  Separate fields with sep. Follow last field with lastSep. */
 
 #define bigTransMapTabOut(el,f) bigTransMapOutput(el,f,'\t','\n');
 /* Print out bigTransMap as a line in a tab-separated file. */
 
 #define bigTransMapCommaOut(el,f) bigTransMapOutput(el,f,',',',');
 /* Print out bigTransMap as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 #endif /* BIGTRANSMAP_H */