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/lib/genomicSuperDups.c src/hg/lib/genomicSuperDups.c
deleted file mode 100644
index ba0ce26..0000000
--- src/hg/lib/genomicSuperDups.c
+++ /dev/null
@@ -1,286 +0,0 @@
-/* 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);
-}
-