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
@@ -1,204 +1,204 @@
 /* wgEncodeGencodeAttrs.c was originally generated by the autoSql program, which also 
  * generated wgEncodeGencodeAttrs.h and wgEncodeGencodeAttrs.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "encode/wgEncodeGencodeAttrs.h"
 
 
 
 char *wgEncodeGencodeAttrsCommaSepFieldNames = "geneId,geneName,geneType,geneStatus,transcriptId,transcriptName,transcriptType,transcriptStatus,havanaGeneId,havanaTranscriptId,ccdsId,level,transcriptClass,proteinId,transcriptRank";
 
 void wgEncodeGencodeAttrsStaticLoad(char **row, int numColumns, struct wgEncodeGencodeAttrs *ret)
 /* Load a row from wgEncodeGencodeAttrs table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->geneId = row[0];
 ret->geneName = row[1];
 ret->geneType = row[2];
 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);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct wgEncodeGencodeAttrs *wgEncodeGencodeAttrsLoadAllByChar(char *fileName, char chopper) 
 /* Load all wgEncodeGencodeAttrs from a chopper separated file.
  * Dispose of this with wgEncodeGencodeAttrsFreeList(). */
 {
 struct wgEncodeGencodeAttrs *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[14];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = wgEncodeGencodeAttrsLoad(row, WGENCODEGENCODEATTRS_NUM_COLS);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 void wgEncodeGencodeAttrsFree(struct wgEncodeGencodeAttrs **pEl)
 /* Free a single dynamically allocated wgEncodeGencodeAttrs such as created
  * with wgEncodeGencodeAttrsLoad(). */
 {
 struct wgEncodeGencodeAttrs *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->geneId);
 freeMem(el->geneName);
 freeMem(el->geneType);
 freeMem(el->geneStatus);
 freeMem(el->transcriptId);
 freeMem(el->transcriptName);
 freeMem(el->transcriptType);
 freeMem(el->transcriptStatus);
 freeMem(el->havanaGeneId);
 freeMem(el->havanaTranscriptId);
 freeMem(el->ccdsId);
 freeMem(el->transcriptClass);
 freeMem(el->proteinId);
 freez(pEl);
 }
 
 void wgEncodeGencodeAttrsFreeList(struct wgEncodeGencodeAttrs **pList)
 /* Free a list of dynamically allocated wgEncodeGencodeAttrs's */
 {
 struct wgEncodeGencodeAttrs *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     wgEncodeGencodeAttrsFree(&el);
     }
 *pList = NULL;
 }
 
 void wgEncodeGencodeAttrsOutput(struct wgEncodeGencodeAttrs *el, FILE *f, char sep, char lastSep) 
 /* Print out wgEncodeGencodeAttrs.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneStatus);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->transcriptId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->transcriptName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->transcriptType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->transcriptStatus);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->havanaGeneId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->havanaTranscriptId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ccdsId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->level);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->transcriptClass);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->proteinId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->transcriptRank);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */