ca39d76b0c4deafcb785e8bea631d316b3bb59ed
markd
  Fri Oct 28 21:28:51 2022 -0700
import of GENCODE V42 final release with addition of transcript rankings

diff --git src/hg/lib/encode/wgEncodeGencodeAttrs.c src/hg/lib/encode/wgEncodeGencodeAttrs.c
index 6ba7f95..c2c116e 100644
--- src/hg/lib/encode/wgEncodeGencodeAttrs.c
+++ src/hg/lib/encode/wgEncodeGencodeAttrs.c
@@ -23,59 +23,59 @@
 ret->geneStatus = row[3];
 ret->transcriptId = row[4];
 ret->transcriptName = row[5];
 ret->transcriptType = row[6];
 ret->transcriptStatus = row[7];
 ret->havanaGeneId = row[8];
 ret->havanaTranscriptId = row[9];
 ret->ccdsId = row[10];
 ret->level = sqlSigned(row[11]);
 ret->transcriptClass = row[12];
 if (numColumns > 13)
     ret->proteinId = row[13];
 if (numColumns > 14)
     ret->transcriptRank = sqlSigned(row[14]);
 else
-    ret->transcriptRank = -1;
+    ret->transcriptRank = 0;
 }
 
 struct wgEncodeGencodeAttrs *wgEncodeGencodeAttrsLoad(char **row, int numColumns)
 /* Load a wgEncodeGencodeAttrs from row fetched with select * from wgEncodeGencodeAttrs
  * from database.  Dispose of this with wgEncodeGencodeAttrsFree(). */
 {
 struct wgEncodeGencodeAttrs *ret;
 
 AllocVar(ret);
 ret->geneId = cloneString(row[0]);
 ret->geneName = cloneString(row[1]);
 ret->geneType = cloneString(row[2]);
 ret->geneStatus = cloneString(row[3]);
 ret->transcriptId = cloneString(row[4]);
 ret->transcriptName = cloneString(row[5]);
 ret->transcriptType = cloneString(row[6]);
 ret->transcriptStatus = cloneString(row[7]);
 ret->havanaGeneId = cloneString(row[8]);
 ret->havanaTranscriptId = cloneString(row[9]);
 ret->ccdsId = cloneString(row[10]);
 ret->level = sqlSigned(row[11]);
 ret->transcriptClass = cloneString(row[12]);
 if (numColumns > 13)
     ret->proteinId = cloneString(row[13]);
 if (numColumns > 14)
     ret->transcriptRank = sqlSigned(row[14]);
 else
-    ret->transcriptRank = -1;
+    ret->transcriptRank = 0;
 return ret;
 }
 
 struct wgEncodeGencodeAttrs *wgEncodeGencodeAttrsLoadAll(char *fileName) 
 /* Load all wgEncodeGencodeAttrs from a whitespace-separated file.
  * Dispose of this with wgEncodeGencodeAttrsFreeList(). */
 {
 struct wgEncodeGencodeAttrs *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[14];
 
 while (lineFileRow(lf, row))
     {
     el = wgEncodeGencodeAttrsLoad(row, WGENCODEGENCODEATTRS_NUM_COLS);
     slAddHead(&list, el);