a93daa92b77f5717f8ff247cb049a46cd0f66409
markd
  Sun Aug 21 17:37:28 2022 -0700
add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution.  Import GENCODE V42 prerelease to test out creating column

diff --git src/hg/lib/encode/wgEncodeGencodeAttrs.c src/hg/lib/encode/wgEncodeGencodeAttrs.c
index 51ba441..6ba7f95 100644
--- src/hg/lib/encode/wgEncodeGencodeAttrs.c
+++ src/hg/lib/encode/wgEncodeGencodeAttrs.c
@@ -1,73 +1,81 @@
 /* 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";
+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;
 }
 
 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;
 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);
@@ -83,57 +91,30 @@
 {
 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;
 }
 
-struct wgEncodeGencodeAttrs *wgEncodeGencodeAttrsCommaIn(char **pS, struct wgEncodeGencodeAttrs *ret)
-/* Create a wgEncodeGencodeAttrs out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new wgEncodeGencodeAttrs */
-{
-char *s = *pS;
-
-if (ret == NULL)
-    AllocVar(ret);
-ret->geneId = sqlStringComma(&s);
-ret->geneName = sqlStringComma(&s);
-ret->geneType = sqlStringComma(&s);
-ret->geneStatus = sqlStringComma(&s);
-ret->transcriptId = sqlStringComma(&s);
-ret->transcriptName = sqlStringComma(&s);
-ret->transcriptType = sqlStringComma(&s);
-ret->transcriptStatus = sqlStringComma(&s);
-ret->havanaGeneId = sqlStringComma(&s);
-ret->havanaTranscriptId = sqlStringComma(&s);
-ret->ccdsId = sqlStringComma(&s);
-ret->level = sqlSignedComma(&s);
-ret->transcriptClass = sqlStringComma(&s);
-ret->proteinId = sqlStringComma(&s);
-*pS = s;
-return ret;
-}
-
 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);
@@ -202,20 +183,22 @@
 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 -------------------------------- */