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) 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 */