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/genomicSuperDups.c src/hg/cgilib/genomicSuperDups.c
new file mode 100644
index 0000000..ba0ce26
--- /dev/null
+++ src/hg/cgilib/genomicSuperDups.c
@@ -0,0 +1,286 @@
+/* genomicSuperDups.c was originally generated by the autoSql program, which also 
+ * generated genomicSuperDups.h and genomicSuperDups.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 "genomicSuperDups.h"
+
+
+void genomicSuperDupsStaticLoad(char **row, struct genomicSuperDups *ret)
+/* Load a row from genomicSuperDups 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]);
+strcpy(ret->strand, row[5]);
+ret->otherChrom = row[6];
+ret->otherStart = sqlUnsigned(row[7]);
+ret->otherEnd = sqlUnsigned(row[8]);
+ret->otherSize = sqlUnsigned(row[9]);
+ret->uid = sqlUnsigned(row[10]);
+ret->posBasesHit = sqlUnsigned(row[11]);
+ret->testResult = row[12];
+ret->verdict = row[13];
+ret->chits = row[14];
+ret->ccov = row[15];
+ret->alignfile = row[16];
+ret->alignL = sqlUnsigned(row[17]);
+ret->indelN = sqlUnsigned(row[18]);
+ret->indelS = sqlUnsigned(row[19]);
+ret->alignB = sqlUnsigned(row[20]);
+ret->matchB = sqlUnsigned(row[21]);
+ret->mismatchB = sqlUnsigned(row[22]);
+ret->transitionsB = sqlUnsigned(row[23]);
+ret->transversionsB = sqlUnsigned(row[24]);
+ret->fracMatch = atof(row[25]);
+ret->fracMatchIndel = atof(row[26]);
+ret->jcK = atof(row[27]);
+ret->k2K = atof(row[28]);
+}
+
+struct genomicSuperDups *genomicSuperDupsLoad(char **row)
+/* Load a genomicSuperDups from row fetched with select * from genomicSuperDups
+ * from database.  Dispose of this with genomicSuperDupsFree(). */
+{
+struct genomicSuperDups *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]);
+strcpy(ret->strand, row[5]);
+ret->otherChrom = cloneString(row[6]);
+ret->otherStart = sqlUnsigned(row[7]);
+ret->otherEnd = sqlUnsigned(row[8]);
+ret->otherSize = sqlUnsigned(row[9]);
+ret->uid = sqlUnsigned(row[10]);
+ret->posBasesHit = sqlUnsigned(row[11]);
+ret->testResult = cloneString(row[12]);
+ret->verdict = cloneString(row[13]);
+ret->chits = cloneString(row[14]);
+ret->ccov = cloneString(row[15]);
+ret->alignfile = cloneString(row[16]);
+ret->alignL = sqlUnsigned(row[17]);
+ret->indelN = sqlUnsigned(row[18]);
+ret->indelS = sqlUnsigned(row[19]);
+ret->alignB = sqlUnsigned(row[20]);
+ret->matchB = sqlUnsigned(row[21]);
+ret->mismatchB = sqlUnsigned(row[22]);
+ret->transitionsB = sqlUnsigned(row[23]);
+ret->transversionsB = sqlUnsigned(row[24]);
+ret->fracMatch = atof(row[25]);
+ret->fracMatchIndel = atof(row[26]);
+ret->jcK = atof(row[27]);
+ret->k2K = atof(row[28]);
+return ret;
+}
+
+struct genomicSuperDups *genomicSuperDupsLoadAll(char *fileName) 
+/* Load all genomicSuperDups from a tab-separated file.
+ * Dispose of this with genomicSuperDupsFreeList(). */
+{
+struct genomicSuperDups *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[29];
+
+while (lineFileRow(lf, row))
+    {
+    el = genomicSuperDupsLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct genomicSuperDups *genomicSuperDupsLoadWhere(struct sqlConnection *conn, char *table, char *where)
+/* Load all genomicSuperDups from table that satisfy where clause. The
+ * where clause may be NULL in which case whole table is loaded
+ * Dispose of this with genomicSuperDupsFreeList(). */
+{
+struct genomicSuperDups *list = NULL, *el;
+struct dyString *query = dyStringNew(256);
+struct sqlResult *sr;
+char **row;
+
+sqlDyStringPrintf(query, "select * from %s", table);
+if (where != NULL)
+    dyStringPrintf(query, " where %s", where);
+sr = sqlGetResult(conn, query->string);
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    el = genomicSuperDupsLoad(row);
+    slAddHead(&list, el);
+    }
+slReverse(&list);
+sqlFreeResult(&sr);
+dyStringFree(&query);
+return list;
+}
+
+struct genomicSuperDups *genomicSuperDupsCommaIn(char **pS, struct genomicSuperDups *ret)
+/* Create a genomicSuperDups out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new genomicSuperDups */
+{
+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->otherChrom = sqlStringComma(&s);
+ret->otherStart = sqlUnsignedComma(&s);
+ret->otherEnd = sqlUnsignedComma(&s);
+ret->otherSize = sqlUnsignedComma(&s);
+ret->uid = sqlUnsignedComma(&s);
+ret->posBasesHit = sqlUnsignedComma(&s);
+ret->testResult = sqlStringComma(&s);
+ret->verdict = sqlStringComma(&s);
+ret->chits = sqlStringComma(&s);
+ret->ccov = sqlStringComma(&s);
+ret->alignfile = sqlStringComma(&s);
+ret->alignL = sqlUnsignedComma(&s);
+ret->indelN = sqlUnsignedComma(&s);
+ret->indelS = sqlUnsignedComma(&s);
+ret->alignB = sqlUnsignedComma(&s);
+ret->matchB = sqlUnsignedComma(&s);
+ret->mismatchB = sqlUnsignedComma(&s);
+ret->transitionsB = sqlUnsignedComma(&s);
+ret->transversionsB = sqlUnsignedComma(&s);
+ret->fracMatch = sqlFloatComma(&s);
+ret->fracMatchIndel = sqlFloatComma(&s);
+ret->jcK = sqlFloatComma(&s);
+ret->k2K = sqlFloatComma(&s);
+*pS = s;
+return ret;
+}
+
+void genomicSuperDupsFree(struct genomicSuperDups **pEl)
+/* Free a single dynamically allocated genomicSuperDups such as created
+ * with genomicSuperDupsLoad(). */
+{
+struct genomicSuperDups *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->otherChrom);
+freeMem(el->testResult);
+freeMem(el->verdict);
+freeMem(el->chits);
+freeMem(el->ccov);
+freeMem(el->alignfile);
+freez(pEl);
+}
+
+void genomicSuperDupsFreeList(struct genomicSuperDups **pList)
+/* Free a list of dynamically allocated genomicSuperDups's */
+{
+struct genomicSuperDups *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    genomicSuperDupsFree(&el);
+    }
+*pList = NULL;
+}
+
+void genomicSuperDupsOutput(struct genomicSuperDups *el, FILE *f, char sep, char lastSep) 
+/* Print out genomicSuperDups.  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->otherChrom);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->otherStart);
+fputc(sep,f);
+fprintf(f, "%u", el->otherEnd);
+fputc(sep,f);
+fprintf(f, "%u", el->otherSize);
+fputc(sep,f);
+fprintf(f, "%u", el->uid);
+fputc(sep,f);
+fprintf(f, "%u", el->posBasesHit);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->testResult);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->verdict);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->chits);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->ccov);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->alignfile);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->alignL);
+fputc(sep,f);
+fprintf(f, "%u", el->indelN);
+fputc(sep,f);
+fprintf(f, "%u", el->indelS);
+fputc(sep,f);
+fprintf(f, "%u", el->alignB);
+fputc(sep,f);
+fprintf(f, "%u", el->matchB);
+fputc(sep,f);
+fprintf(f, "%u", el->mismatchB);
+fputc(sep,f);
+fprintf(f, "%u", el->transitionsB);
+fputc(sep,f);
+fprintf(f, "%u", el->transversionsB);
+fputc(sep,f);
+fprintf(f, "%f", el->fracMatch);
+fputc(sep,f);
+fprintf(f, "%f", el->fracMatchIndel);
+fputc(sep,f);
+fprintf(f, "%f", el->jcK);
+fputc(sep,f);
+fprintf(f, "%f", el->k2K);
+fputc(lastSep,f);
+}
+