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/hapmapAlleles.c src/hg/lib/hapmapAlleles.c
index 68cf967..bcc956c 100644
--- src/hg/lib/hapmapAlleles.c
+++ src/hg/lib/hapmapAlleles.c
@@ -1,183 +1,186 @@
 /* hapmapAlleles.c was originally generated by the autoSql program, which also 
  * generated hapmapAlleles.h and hapmapAlleles.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 "hapmapAlleles.h"
 
 
 void hapmapAllelesStaticLoad(char **row, struct hapmapAlleles *ret)
 /* Load a row from hapmapAlleles 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->homoCount1 = sqlUnsigned(row[8]);
 ret->allele2 = row[9];
 ret->homoCount2 = sqlUnsigned(row[10]);
 ret->heteroCount = sqlUnsigned(row[11]);
 }
 
 struct hapmapAlleles *hapmapAllelesLoad(char **row)
 /* Load a hapmapAlleles from row fetched with select * from hapmapAlleles
  * from database.  Dispose of this with hapmapAllelesFree(). */
 {
 struct hapmapAlleles *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->homoCount1 = sqlUnsigned(row[8]);
 ret->allele2 = cloneString(row[9]);
 ret->homoCount2 = sqlUnsigned(row[10]);
 ret->heteroCount = sqlUnsigned(row[11]);
 return ret;
 }
 
 struct hapmapAlleles *hapmapAllelesLoadAll(char *fileName) 
 /* Load all hapmapAlleles from a whitespace-separated file.
  * Dispose of this with hapmapAllelesFreeList(). */
 {
 struct hapmapAlleles *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileRow(lf, row))
     {
     el = hapmapAllelesLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hapmapAlleles *hapmapAllelesLoadAllByChar(char *fileName, char chopper) 
 /* Load all hapmapAlleles from a chopper separated file.
  * Dispose of this with hapmapAllelesFreeList(). */
 {
 struct hapmapAlleles *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = hapmapAllelesLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hapmapAlleles *hapmapAllelesCommaIn(char **pS, struct hapmapAlleles *ret)
 /* Create a hapmapAlleles out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new hapmapAlleles */
 {
 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->homoCount1 = sqlUnsignedComma(&s);
 ret->allele2 = sqlStringComma(&s);
 ret->homoCount2 = sqlUnsignedComma(&s);
 ret->heteroCount = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void hapmapAllelesFree(struct hapmapAlleles **pEl)
 /* Free a single dynamically allocated hapmapAlleles such as created
  * with hapmapAllelesLoad(). */
 {
 struct hapmapAlleles *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->observed);
 freeMem(el->allele2);
 freez(pEl);
 }
 
 void hapmapAllelesFreeList(struct hapmapAlleles **pList)
 /* Free a list of dynamically allocated hapmapAlleles's */
 {
 struct hapmapAlleles *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     hapmapAllelesFree(&el);
     }
 *pList = NULL;
 }
 
 void hapmapAllelesOutput(struct hapmapAlleles *el, FILE *f, char sep, char lastSep) 
 /* Print out hapmapAlleles.  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);
 fprintf(f, "%u", el->homoCount1);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->allele2);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->homoCount2);
 fputc(sep,f);
 fprintf(f, "%u", el->heteroCount);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */