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/hapmapPhaseIIISummary.c src/hg/lib/hapmapPhaseIIISummary.c
index 0fb913c..6358e19 100644
--- src/hg/lib/hapmapPhaseIIISummary.c
+++ src/hg/lib/hapmapPhaseIIISummary.c
@@ -1,271 +1,274 @@
 /* hapmapPhaseIIISummary.c was originally generated by the autoSql program, which also 
  * generated hapmapPhaseIIISummary.h and hapmapPhaseIIISummary.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 "hapmapPhaseIIISummary.h"
 
 
 struct hapmapPhaseIIISummary *hapmapPhaseIIISummaryLoad(char **row)
 /* Load a hapmapPhaseIIISummary from row fetched with select * from hapmapPhaseIIISummary
  * from database.  Dispose of this with hapmapPhaseIIISummaryFree(). */
 {
 struct hapmapPhaseIIISummary *ret;
 
 AllocVar(ret);
 ret->orthoCount = sqlUnsigned(row[15]);
 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]);
 ret->observed = cloneString(row[5]);
 ret->overallMajorAllele = row[6][0];
 ret->overallMinorAllele = row[7][0];
 ret->popCount = sqlUnsigned(row[8]);
 ret->phaseIIPopCount = sqlUnsigned(row[9]);
 ret->isMixed = sqlUnsigned(row[10]);
 sqlUbyteArray(row[11], ret->foundInPop, 11);
 sqlUbyteArray(row[12], ret->monomorphicInPop, 11);
 ret->minFreq = sqlFloat(row[13]);
 ret->maxFreq = sqlFloat(row[14]);
 {
 int sizeOne;
 sqlCharDynamicArray(row[16], &ret->orthoAlleles, &sizeOne);
 assert(sizeOne == ret->orthoCount);
 }
 {
 int sizeOne;
 sqlUshortDynamicArray(row[17], &ret->orthoQuals, &sizeOne);
 assert(sizeOne == ret->orthoCount);
 }
 return ret;
 }
 
 struct hapmapPhaseIIISummary *hapmapPhaseIIISummaryLoadAll(char *fileName) 
 /* Load all hapmapPhaseIIISummary from a whitespace-separated file.
  * Dispose of this with hapmapPhaseIIISummaryFreeList(). */
 {
 struct hapmapPhaseIIISummary *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileRow(lf, row))
     {
     el = hapmapPhaseIIISummaryLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hapmapPhaseIIISummary *hapmapPhaseIIISummaryLoadAllByChar(char *fileName, char chopper) 
 /* Load all hapmapPhaseIIISummary from a chopper separated file.
  * Dispose of this with hapmapPhaseIIISummaryFreeList(). */
 {
 struct hapmapPhaseIIISummary *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = hapmapPhaseIIISummaryLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hapmapPhaseIIISummary *hapmapPhaseIIISummaryCommaIn(char **pS, struct hapmapPhaseIIISummary *ret)
 /* Create a hapmapPhaseIIISummary out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new hapmapPhaseIIISummary */
 {
 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);
 ret->observed = sqlStringComma(&s);
 sqlFixedStringComma(&s, &(ret->overallMajorAllele), sizeof(ret->overallMajorAllele));
 sqlFixedStringComma(&s, &(ret->overallMinorAllele), sizeof(ret->overallMinorAllele));
 ret->popCount = sqlUnsignedComma(&s);
 ret->phaseIIPopCount = sqlUnsignedComma(&s);
 ret->isMixed = sqlUnsignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 for (i=0; i<11; ++i)
     {
     ret->foundInPop[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 for (i=0; i<11; ++i)
     {
     ret->monomorphicInPop[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->minFreq = sqlFloatComma(&s);
 ret->maxFreq = sqlFloatComma(&s);
 ret->orthoCount = sqlUnsignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->orthoAlleles, ret->orthoCount);
 for (i=0; i<ret->orthoCount; ++i)
     {
     ret->orthoAlleles[i] = sqlCharComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->orthoQuals, ret->orthoCount);
 for (i=0; i<ret->orthoCount; ++i)
     {
     ret->orthoQuals[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 *pS = s;
 return ret;
 }
 
 void hapmapPhaseIIISummaryFree(struct hapmapPhaseIIISummary **pEl)
 /* Free a single dynamically allocated hapmapPhaseIIISummary such as created
  * with hapmapPhaseIIISummaryLoad(). */
 {
 struct hapmapPhaseIIISummary *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->observed);
 freeMem(el->orthoAlleles);
 freeMem(el->orthoQuals);
 freez(pEl);
 }
 
 void hapmapPhaseIIISummaryFreeList(struct hapmapPhaseIIISummary **pList)
 /* Free a list of dynamically allocated hapmapPhaseIIISummary's */
 {
 struct hapmapPhaseIIISummary *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     hapmapPhaseIIISummaryFree(&el);
     }
 *pList = NULL;
 }
 
 void hapmapPhaseIIISummaryOutput(struct hapmapPhaseIIISummary *el, FILE *f, char sep, char lastSep) 
 /* Print out hapmapPhaseIIISummary.  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->observed);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->overallMajorAllele);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->overallMinorAllele);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->popCount);
 fputc(sep,f);
 fprintf(f, "%u", el->phaseIIPopCount);
 fputc(sep,f);
 fprintf(f, "%u", el->isMixed);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<11; ++i)
     {
     fprintf(f, "%u", el->foundInPop[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<11; ++i)
     {
     fprintf(f, "%u", el->monomorphicInPop[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 fprintf(f, "%g", el->minFreq);
 fputc(sep,f);
 fprintf(f, "%g", el->maxFreq);
 fputc(sep,f);
 fprintf(f, "%u", el->orthoCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->orthoCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%c", el->orthoAlleles[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->orthoCount; ++i)
     {
     fprintf(f, "%u", el->orthoQuals[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */