e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/lib/hapmapAllelesSummary.c src/hg/lib/hapmapAllelesSummary.c
index b134f90..d8ca98b 100644
--- src/hg/lib/hapmapAllelesSummary.c
+++ src/hg/lib/hapmapAllelesSummary.c
@@ -1,279 +1,282 @@
 /* hapmapAllelesSummary.c was originally generated by the autoSql program, which also 
  * generated hapmapAllelesSummary.h and hapmapAllelesSummary.sql.  This module links the database and
  * the RAM representation of objects. */
 
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "hapmapAllelesSummary.h"
 
 
 void hapmapAllelesSummaryStaticLoad(char **row, struct hapmapAllelesSummary *ret)
 /* Load a row from hapmapAllelesSummary table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->observed = row[6];
 safecpy(ret->allele1, sizeof(ret->allele1), row[7]);
 ret->allele2 = row[8];
 ret->popCount = sqlUnsigned(row[9]);
 ret->isMixed = row[10];
 ret->majorAlleleCEU = row[11];
 ret->majorAlleleCountCEU = sqlUnsigned(row[12]);
 ret->totalAlleleCountCEU = sqlUnsigned(row[13]);
 ret->majorAlleleCHB = row[14];
 ret->majorAlleleCountCHB = sqlUnsigned(row[15]);
 ret->totalAlleleCountCHB = sqlUnsigned(row[16]);
 ret->majorAlleleJPT = row[17];
 ret->majorAlleleCountJPT = sqlUnsigned(row[18]);
 ret->totalAlleleCountJPT = sqlUnsigned(row[19]);
 ret->majorAlleleYRI = row[20];
 ret->majorAlleleCountYRI = sqlUnsigned(row[21]);
 ret->totalAlleleCountYRI = sqlUnsigned(row[22]);
 ret->chimpAllele = row[23];
 ret->chimpAlleleQuality = sqlUnsigned(row[24]);
 ret->macaqueAllele = row[25];
 ret->macaqueAlleleQuality = sqlUnsigned(row[26]);
 }
 
 struct hapmapAllelesSummary *hapmapAllelesSummaryLoad(char **row)
 /* Load a hapmapAllelesSummary from row fetched with select * from hapmapAllelesSummary
  * from database.  Dispose of this with hapmapAllelesSummaryFree(). */
 {
 struct hapmapAllelesSummary *ret;
 
 AllocVar(ret);
 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->observed = cloneString(row[6]);
 safecpy(ret->allele1, sizeof(ret->allele1), row[7]);
 ret->allele2 = cloneString(row[8]);
 ret->popCount = sqlUnsigned(row[9]);
 ret->isMixed = cloneString(row[10]);
 ret->majorAlleleCEU = cloneString(row[11]);
 ret->majorAlleleCountCEU = sqlUnsigned(row[12]);
 ret->totalAlleleCountCEU = sqlUnsigned(row[13]);
 ret->majorAlleleCHB = cloneString(row[14]);
 ret->majorAlleleCountCHB = sqlUnsigned(row[15]);
 ret->totalAlleleCountCHB = sqlUnsigned(row[16]);
 ret->majorAlleleJPT = cloneString(row[17]);
 ret->majorAlleleCountJPT = sqlUnsigned(row[18]);
 ret->totalAlleleCountJPT = sqlUnsigned(row[19]);
 ret->majorAlleleYRI = cloneString(row[20]);
 ret->majorAlleleCountYRI = sqlUnsigned(row[21]);
 ret->totalAlleleCountYRI = sqlUnsigned(row[22]);
 ret->chimpAllele = cloneString(row[23]);
 ret->chimpAlleleQuality = sqlUnsigned(row[24]);
 ret->macaqueAllele = cloneString(row[25]);
 ret->macaqueAlleleQuality = sqlUnsigned(row[26]);
 return ret;
 }
 
 struct hapmapAllelesSummary *hapmapAllelesSummaryLoadAll(char *fileName) 
 /* Load all hapmapAllelesSummary from a whitespace-separated file.
  * Dispose of this with hapmapAllelesSummaryFreeList(). */
 {
 struct hapmapAllelesSummary *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[27];
 
 while (lineFileRow(lf, row))
     {
     el = hapmapAllelesSummaryLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hapmapAllelesSummary *hapmapAllelesSummaryLoadAllByChar(char *fileName, char chopper) 
 /* Load all hapmapAllelesSummary from a chopper separated file.
  * Dispose of this with hapmapAllelesSummaryFreeList(). */
 {
 struct hapmapAllelesSummary *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[27];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = hapmapAllelesSummaryLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hapmapAllelesSummary *hapmapAllelesSummaryCommaIn(char **pS, struct hapmapAllelesSummary *ret)
 /* Create a hapmapAllelesSummary out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new hapmapAllelesSummary */
 {
 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->observed = sqlStringComma(&s);
 sqlFixedStringComma(&s, ret->allele1, sizeof(ret->allele1));
 ret->allele2 = sqlStringComma(&s);
 ret->popCount = sqlUnsignedComma(&s);
 ret->isMixed = sqlStringComma(&s);
 ret->majorAlleleCEU = sqlStringComma(&s);
 ret->majorAlleleCountCEU = sqlUnsignedComma(&s);
 ret->totalAlleleCountCEU = sqlUnsignedComma(&s);
 ret->majorAlleleCHB = sqlStringComma(&s);
 ret->majorAlleleCountCHB = sqlUnsignedComma(&s);
 ret->totalAlleleCountCHB = sqlUnsignedComma(&s);
 ret->majorAlleleJPT = sqlStringComma(&s);
 ret->majorAlleleCountJPT = sqlUnsignedComma(&s);
 ret->totalAlleleCountJPT = sqlUnsignedComma(&s);
 ret->majorAlleleYRI = sqlStringComma(&s);
 ret->majorAlleleCountYRI = sqlUnsignedComma(&s);
 ret->totalAlleleCountYRI = sqlUnsignedComma(&s);
 ret->chimpAllele = sqlStringComma(&s);
 ret->chimpAlleleQuality = sqlUnsignedComma(&s);
 ret->macaqueAllele = sqlStringComma(&s);
 ret->macaqueAlleleQuality = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void hapmapAllelesSummaryFree(struct hapmapAllelesSummary **pEl)
 /* Free a single dynamically allocated hapmapAllelesSummary such as created
  * with hapmapAllelesSummaryLoad(). */
 {
 struct hapmapAllelesSummary *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->observed);
 freeMem(el->allele2);
 freeMem(el->isMixed);
 freeMem(el->majorAlleleCEU);
 freeMem(el->majorAlleleCHB);
 freeMem(el->majorAlleleJPT);
 freeMem(el->majorAlleleYRI);
 freeMem(el->chimpAllele);
 freeMem(el->macaqueAllele);
 freez(pEl);
 }
 
 void hapmapAllelesSummaryFreeList(struct hapmapAllelesSummary **pList)
 /* Free a list of dynamically allocated hapmapAllelesSummary's */
 {
 struct hapmapAllelesSummary *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     hapmapAllelesSummaryFree(&el);
     }
 *pList = NULL;
 }
 
 void hapmapAllelesSummaryOutput(struct hapmapAllelesSummary *el, FILE *f, char sep, char lastSep) 
 /* Print out hapmapAllelesSummary.  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->observed);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->allele1);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->allele2);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->popCount);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->isMixed);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->majorAlleleCEU);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->majorAlleleCountCEU);
 fputc(sep,f);
 fprintf(f, "%u", el->totalAlleleCountCEU);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->majorAlleleCHB);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->majorAlleleCountCHB);
 fputc(sep,f);
 fprintf(f, "%u", el->totalAlleleCountCHB);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->majorAlleleJPT);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->majorAlleleCountJPT);
 fputc(sep,f);
 fprintf(f, "%u", el->totalAlleleCountJPT);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->majorAlleleYRI);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->majorAlleleCountYRI);
 fputc(sep,f);
 fprintf(f, "%u", el->totalAlleleCountYRI);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chimpAllele);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chimpAlleleQuality);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->macaqueAllele);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->macaqueAlleleQuality);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */