43af8e2635c1797ee03bf3ded32d795ed4a91ed9
braney
  Wed Sep 10 19:20:24 2014 -0700
add exonFrames to genePreds that don't have them.   #13861
diff --git src/hg/lib/bigGenePred.c src/hg/lib/bigGenePred.c
index c25823b..3731892 100644
--- src/hg/lib/bigGenePred.c
+++ src/hg/lib/bigGenePred.c
@@ -1,289 +1,293 @@
 /* bigGenePred.c was originally generated by the autoSql program, which also 
  * generated bigGenePred.h and bigGenePred.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 "bigGenePred.h"
 
 
 
 char *bigGenePredCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,chromStarts,name2,cdsStartStat,cdsEndStat,exonFrames,type,geneName,geneName2,geneType";
 
 struct bigGenePred *bigGenePredLoad(char **row)
 /* Load a bigGenePred from row fetched with select * from bigGenePred
  * from database.  Dispose of this with bigGenePredFree(). */
 {
 struct bigGenePred *ret;
 
 AllocVar(ret);
 ret->blockCount = sqlSigned(row[9]);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
 ret->itemRgb = sqlUnsigned(row[8]);
 {
 int sizeOne;
 sqlUnsignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
 assert(sizeOne == ret->blockCount);
 }
 {
 int sizeOne;
 sqlUnsignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
 assert(sizeOne == ret->blockCount);
 }
 ret->name2 = cloneString(row[12]);
 ret->cdsStartStat = parseCdsStat(row[13]);
 ret->cdsEndStat = parseCdsStat(row[14]);
 {
 int sizeOne;
 sqlSignedDynamicArray(row[15], &ret->exonFrames, &sizeOne);
 assert(sizeOne == ret->blockCount);
 }
 ret->type = cloneString(row[16]);
 ret->geneName = cloneString(row[17]);
 ret->geneName2 = cloneString(row[18]);
 ret->geneType = cloneString(row[19]);
 return ret;
 }
 
 struct bigGenePred *bigGenePredLoadAll(char *fileName) 
 /* Load all bigGenePred from a whitespace-separated file.
  * Dispose of this with bigGenePredFreeList(). */
 {
 struct bigGenePred *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[20];
 
 while (lineFileRow(lf, row))
     {
     el = bigGenePredLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct bigGenePred *bigGenePredLoadAllByChar(char *fileName, char chopper) 
 /* Load all bigGenePred from a chopper separated file.
  * Dispose of this with bigGenePredFreeList(). */
 {
 struct bigGenePred *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[20];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = bigGenePredLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 #ifdef NOTNOW
 struct bigGenePred *bigGenePredCommaIn(char **pS, struct bigGenePred *ret)
 /* Create a bigGenePred out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new bigGenePred */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->thickStart = sqlUnsignedComma(&s);
 ret->thickEnd = sqlUnsignedComma(&s);
 ret->itemRgb = sqlUnsignedComma(&s);
 ret->blockCount = sqlSignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->blockSizes, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->blockSizes[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->chromStarts, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->chromStarts[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->name2 = sqlStringComma(&s);
 ret->cdsStartStat = parseCdsStat(&s);
 ret->cdsEndStat = parseCdsStat(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->exonFrames, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->exonFrames[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->type = sqlStringComma(&s);
 ret->geneName = sqlStringComma(&s);
 ret->geneName2 = sqlStringComma(&s);
 ret->geneType = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 #endif
 
 void bigGenePredFree(struct bigGenePred **pEl)
 /* Free a single dynamically allocated bigGenePred such as created
  * with bigGenePredLoad(). */
 {
 struct bigGenePred *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->blockSizes);
 freeMem(el->chromStarts);
 freeMem(el->name2);
 freeMem(el->exonFrames);
 freeMem(el->type);
 freeMem(el->geneName);
 freeMem(el->geneName2);
 freeMem(el->geneType);
 freez(pEl);
 }
 
 void bigGenePredFreeList(struct bigGenePred **pList)
 /* Free a list of dynamically allocated bigGenePred's */
 {
 struct bigGenePred *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     bigGenePredFree(&el);
     }
 *pList = NULL;
 }
 
 void bigGenePredOutput(struct bigGenePred *el, FILE *f, char sep, char lastSep) 
 /* Print out bigGenePred.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
+if (el->name != NULL)
     fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->thickStart);
 fputc(sep,f);
 fprintf(f, "%u", el->thickEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->itemRgb);
 fputc(sep,f);
 fprintf(f, "%d", el->blockCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%d", el->blockSizes[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%d", el->chromStarts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 if (el->name2 != NULL)
     fprintf(f, "%s", el->name2);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", genePredCdsStatStr(el->cdsStartStat));
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", genePredCdsStatStr(el->cdsEndStat));
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     if (el->exonFrames != NULL)
 	fprintf(f, "%d", el->exonFrames[i]);
     else
 	fputs("-1", f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
+if (el->type != NULL)
     fprintf(f, "%s", el->type);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
+if (el->geneName != NULL)
     fprintf(f, "%s", el->geneName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 if (el->geneName2 != NULL)
     fprintf(f, "%s", el->geneName2);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
+if (el->geneType != NULL)
     fprintf(f, "%s", el->geneType);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */