03fcdcc33cd21dad46aa78556cdb1d87ce37f144
markd
  Mon Aug 31 12:17:03 2020 -0700
make gencodeV35Attrs more compatible with older tables

diff --git src/hg/lib/gencodeAttrs.c src/hg/lib/gencodeAttrs.c
index 151e687..1bf9f07 100644
--- src/hg/lib/gencodeAttrs.c
+++ src/hg/lib/gencodeAttrs.c
@@ -1,141 +1,157 @@
 /* gencodeAttrs.c was originally generated by the autoSql program, which also 
  * generated gencodeAttrs.h and gencodeAttrs.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 "gencodeAttrs.h"
 
 
 
-char *gencodeAttrsCommaSepFieldNames = "geneId,geneName,geneType,transcriptId,transcriptName,transcriptType,ccdsId,level,proteinId,transcriptClass";
+char *gencodeAttrsCommaSepFieldNames = "geneId,geneName,geneType,unused1,transcriptId,transcriptName,transcriptType,unused2,unused3,unused4,ccdsId,level,transcriptClass,proteinId";
 
 void gencodeAttrsStaticLoad(char **row, struct gencodeAttrs *ret)
 /* Load a row from gencodeAttrs 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->transcriptId = row[3];
-ret->transcriptName = row[4];
-ret->transcriptType = row[5];
-ret->ccdsId = row[6];
-ret->level = sqlSigned(row[7]);
-ret->proteinId = row[8];
-ret->transcriptClass = row[9];
+ret->unused1 = row[3];
+ret->transcriptId = row[4];
+ret->transcriptName = row[5];
+ret->transcriptType = row[6];
+ret->unused2 = row[7];
+ret->unused3 = row[8];
+ret->unused4 = row[9];
+ret->ccdsId = row[10];
+ret->level = sqlSigned(row[11]);
+ret->transcriptClass = row[12];
+ret->proteinId = row[13];
 }
 
 struct gencodeAttrs *gencodeAttrsLoad(char **row)
 /* Load a gencodeAttrs from row fetched with select * from gencodeAttrs
  * from database.  Dispose of this with gencodeAttrsFree(). */
 {
 struct gencodeAttrs *ret;
 
 AllocVar(ret);
 ret->geneId = cloneString(row[0]);
 ret->geneName = cloneString(row[1]);
 ret->geneType = cloneString(row[2]);
-ret->transcriptId = cloneString(row[3]);
-ret->transcriptName = cloneString(row[4]);
-ret->transcriptType = cloneString(row[5]);
-ret->ccdsId = cloneString(row[6]);
-ret->level = sqlSigned(row[7]);
-ret->proteinId = cloneString(row[8]);
-ret->transcriptClass = cloneString(row[9]);
+ret->unused1 = cloneString(row[3]);
+ret->transcriptId = cloneString(row[4]);
+ret->transcriptName = cloneString(row[5]);
+ret->transcriptType = cloneString(row[6]);
+ret->unused2 = cloneString(row[7]);
+ret->unused3 = cloneString(row[8]);
+ret->unused4 = cloneString(row[9]);
+ret->ccdsId = cloneString(row[10]);
+ret->level = sqlSigned(row[11]);
+ret->transcriptClass = cloneString(row[12]);
+ret->proteinId = cloneString(row[13]);
 return ret;
 }
 
 struct gencodeAttrs *gencodeAttrsLoadAll(char *fileName) 
 /* Load all gencodeAttrs from a whitespace-separated file.
  * Dispose of this with gencodeAttrsFreeList(). */
 {
 struct gencodeAttrs *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[10];
+char *row[14];
 
 while (lineFileRow(lf, row))
     {
     el = gencodeAttrsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gencodeAttrs *gencodeAttrsLoadAllByChar(char *fileName, char chopper) 
 /* Load all gencodeAttrs from a chopper separated file.
  * Dispose of this with gencodeAttrsFreeList(). */
 {
 struct gencodeAttrs *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[10];
+char *row[14];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = gencodeAttrsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gencodeAttrs *gencodeAttrsCommaIn(char **pS, struct gencodeAttrs *ret)
 /* Create a gencodeAttrs out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new gencodeAttrs */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->geneId = sqlStringComma(&s);
 ret->geneName = sqlStringComma(&s);
 ret->geneType = sqlStringComma(&s);
+ret->unused1 = sqlStringComma(&s);
 ret->transcriptId = sqlStringComma(&s);
 ret->transcriptName = sqlStringComma(&s);
 ret->transcriptType = sqlStringComma(&s);
+ret->unused2 = sqlStringComma(&s);
+ret->unused3 = sqlStringComma(&s);
+ret->unused4 = sqlStringComma(&s);
 ret->ccdsId = sqlStringComma(&s);
 ret->level = sqlSignedComma(&s);
-ret->proteinId = sqlStringComma(&s);
 ret->transcriptClass = sqlStringComma(&s);
+ret->proteinId = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void gencodeAttrsFree(struct gencodeAttrs **pEl)
 /* Free a single dynamically allocated gencodeAttrs such as created
  * with gencodeAttrsLoad(). */
 {
 struct gencodeAttrs *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->geneId);
 freeMem(el->geneName);
 freeMem(el->geneType);
+freeMem(el->unused1);
 freeMem(el->transcriptId);
 freeMem(el->transcriptName);
 freeMem(el->transcriptType);
+freeMem(el->unused2);
+freeMem(el->unused3);
+freeMem(el->unused4);
 freeMem(el->ccdsId);
-freeMem(el->proteinId);
 freeMem(el->transcriptClass);
+freeMem(el->proteinId);
 freez(pEl);
 }
 
 void gencodeAttrsFreeList(struct gencodeAttrs **pList)
 /* Free a list of dynamically allocated gencodeAttrs's */
 {
 struct gencodeAttrs *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     gencodeAttrsFree(&el);
     }
 *pList = NULL;
 }
@@ -144,44 +160,60 @@
 /* Print out gencodeAttrs.  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->unused1);
+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->unused2);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->unused3);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->unused4);
+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->proteinId);
+fprintf(f, "%s", el->transcriptClass);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->transcriptClass);
+fprintf(f, "%s", el->proteinId);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */