533112afe2a2005e80cdb1f82904ea65032d4302
braney
  Sat Oct 2 11:37:34 2021 -0700
split hg/lib into two separate libaries, one only used by the cgis

diff --git src/hg/cgilib/hapmapAllelesSummary.c src/hg/cgilib/hapmapAllelesSummary.c
new file mode 100644
index 0000000..d8ca98b
--- /dev/null
+++ src/hg/cgilib/hapmapAllelesSummary.c
@@ -0,0 +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 -------------------------------- */
+