text: /* gtexGeneBed.c was originally generated by the autoSql program, which also 
   * generated gtexGeneBed.h and gtexGeneBed.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 "gtexGeneBed.h"
  
  
  
  char *gtexGeneBedCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,geneId,transcriptId,transcriptClass,expCount,expScores";
  
  struct gtexGeneBed *gtexGeneBedLoad(char **row)
  /* Load a gtexGeneBed from row fetched with select * from gtexGeneBed
   * from database.  Dispose of this with gtexGeneBedFree(). */
  {
  struct gtexGeneBed *ret;
  
  AllocVar(ret);
  ret->expCount = sqlUnsigned(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->geneId = cloneString(row[6]);
  ret->transcriptId = cloneString(row[7]);
  ret->transcriptClass = cloneString(row[8]);
  {
  int sizeOne;
  sqlFloatDynamicArray(row[10], &ret->expScores, &sizeOne);
  assert(sizeOne == ret->expCount);
  }
  return ret;
  }
  
  struct gtexGeneBed *gtexGeneBedLoadAll(char *fileName) 
  /* Load all gtexGeneBed from a whitespace-separated file.
   * Dispose of this with gtexGeneBedFreeList(). */
  {
  struct gtexGeneBed *list = NULL, *el;
  struct lineFile *lf = lineFileOpen(fileName, TRUE);
  char *row[11];
  
  while (lineFileRow(lf, row))
      {
      el = gtexGeneBedLoad(row);
      slAddHead(&list, el);
      }
  lineFileClose(&lf);
  slReverse(&list);
  return list;
  }
  
  struct gtexGeneBed *gtexGeneBedLoadAllByChar(char *fileName, char chopper) 
  /* Load all gtexGeneBed from a chopper separated file.
   * Dispose of this with gtexGeneBedFreeList(). */
  {
  struct gtexGeneBed *list = NULL, *el;
  struct lineFile *lf = lineFileOpen(fileName, TRUE);
  char *row[11];
  
  while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
      {
      el = gtexGeneBedLoad(row);
      slAddHead(&list, el);
      }
  lineFileClose(&lf);
  slReverse(&list);
  return list;
  }
  
  struct gtexGeneBed *gtexGeneBedCommaIn(char **pS, struct gtexGeneBed *ret)
  /* Create a gtexGeneBed out of a comma separated string. 
   * This will fill in ret if non-null, otherwise will
   * return a new gtexGeneBed */
  {
  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->geneId = sqlStringComma(&s);
  ret->transcriptId = sqlStringComma(&s);
  ret->transcriptClass = sqlStringComma(&s);
  ret->expCount = sqlUnsignedComma(&s);
  {
  int i;
  s = sqlEatChar(s, '{');
  AllocArray(ret->expScores, ret->expCount);
  for (i=0; i<ret->expCount; ++i)
      {
      ret->expScores[i] = sqlFloatComma(&s);
      }
  s = sqlEatChar(s, '}');
  s = sqlEatChar(s, ',');
  }
  *pS = s;
  return ret;
  }
  
  void gtexGeneBedFree(struct gtexGeneBed **pEl)
  /* Free a single dynamically allocated gtexGeneBed such as created
   * with gtexGeneBedLoad(). */
  {
  struct gtexGeneBed *el;
  
  if ((el = *pEl) == NULL) return;
  freeMem(el->chrom);
  freeMem(el->name);
  freeMem(el->geneId);
  freeMem(el->transcriptId);
  freeMem(el->transcriptClass);
  freeMem(el->expScores);
  freez(pEl);
  }
  
  void gtexGeneBedFreeList(struct gtexGeneBed **pList)
  /* Free a list of dynamically allocated gtexGeneBed's */
  {
  struct gtexGeneBed *el, *next;
  
  for (el = *pList; el != NULL; el = next)
      {
      next = el->next;
      gtexGeneBedFree(&el);
      }
  *pList = NULL;
  }
  
  void gtexGeneBedOutput(struct gtexGeneBed *el, FILE *f, char sep, char lastSep) 
  /* Print out gtexGeneBed.  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);
  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);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->geneId);
  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->transcriptClass);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  fprintf(f, "%u", el->expCount);
  fputc(sep,f);
  {
  int i;
  if (sep == ',') fputc('{',f);
  for (i=0; i<el->expCount; ++i)
      {
      fprintf(f, "%g", el->expScores[i]);
      fputc(',', f);
      }
  if (sep == ',') fputc('}',f);
  }
  fputc(lastSep,f);
  }
  
  /* -------------------------------- End autoSql Generated Code -------------------------------- */
  
  void gtexGeneBedCreateTable(struct sqlConnection *conn, char *table)
  /* Create expression record format table of given name. */
  {
  char query[1024];
  
  sqlSafef(query, sizeof(query),
  "CREATE TABLE %s (\n"
  "   chrom varchar(255) not null,	# Reference sequence chromosome or scaffold\n"
  "   chromStart int unsigned not null,	# Start position in chromosome\n"
  "   chromEnd int unsigned not null,	# End position in chromosome\n"
  "   name varchar(255) not null,	# Gene symbol\n"
  "   score int unsigned not null,	# Score from 0-1000\n"
  "   strand char(1) not null,	# + or - for strand\n"
  "   geneId varchar(255) not null,	# Ensembl gene ID, referenced in GTEx data tables\n"
  "   transcriptId varchar(255) not null,	# Ensembl ID of Canonical transcript; determines genomic position\n"
  "   transcriptClass varchar(255) not null,	# GENCODE transcript class (coding, nonCoding, pseudo)\n"
  "   expCount int unsigned not null,	# Number of experiment values\n"
  "   expScores longblob not null,	# Comma separated list of experiment scores\n"
            "#Indices\n"
  "   PRIMARY KEY(geneId)\n"
  ")\n",
      table);
  sqlRemakeTable(conn, table, query);
  }
  