c257290253d707d2fc749e277f7a96c771accb80
mspeir
  Fri Jan 13 13:29:35 2017 -0800
Adding more detail to transcription/coding/exons start/end columns, refs #18548

diff --git src/hg/lib/genePredExt.as src/hg/lib/genePredExt.as
index c9e7976..7f4541d 100644
--- src/hg/lib/genePredExt.as
+++ src/hg/lib/genePredExt.as
@@ -1,20 +1,20 @@
 table genePredExt
 "A gene prediction with some additional info."
     (
     string name;	"Name of gene (usually transcript_id from GTF)"
     string chrom;	"Reference sequence chromosome or scaffold"
     char[1] strand;     "+ or - for strand"
-    uint txStart;	"Transcription start position"
-    uint txEnd;         "Transcription end position"
-    uint cdsStart;	"Coding region start"
-    uint cdsEnd;        "Coding region end"
+    uint txStart;	"Transcription start position (or transcription end position if item is on minus strand)"
+    uint txEnd;         "Transcription end position (or transcription start position if item is on minus strand)"
+    uint cdsStart;	"Coding region start (or coding end position if item is on minus strand)"
+    uint cdsEnd;        "Coding region end (or coding start position if item is on minus strand)"
     uint exonCount;     "Number of exons"
-    uint[exonCount] exonStarts; "Exon start positions"
-    uint[exonCount] exonEnds;   "Exon end positions"
+    uint[exonCount] exonStarts; "Exon start positions (or exon end positions if item is on minus strand)"
+    uint[exonCount] exonEnds;   "Exon end positions (or exon start positions if item is on minus strand)"
     uint score;         "score"
     string name2;       "Alternate name (e.g. gene_id from GTF)"
     string cdsStartStat; "enum('none','unk','incmpl','cmpl')"
     string cdsEndStat;   "enum('none','unk','incmpl','cmpl')"
     int[exonCount] exonFrames; "Exon frame {0,1,2}, or -1 if no frame for exon"
     )