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/gencodeIntron.c src/hg/lib/gencodeIntron.c
deleted file mode 100644
index 34ba349..0000000
--- src/hg/lib/gencodeIntron.c
+++ /dev/null
@@ -1,226 +0,0 @@
-/* gencodeIntron.c was originally generated by the autoSql program, which also 
- * generated gencodeIntron.h and gencodeIntron.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 "gencodeIntron.h"
-
-
-void gencodeIntronStaticLoad(char **row, struct gencodeIntron *ret)
-/* Load a row from gencodeIntron 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->status = row[4];
-strcpy(ret->strand, row[5]);
-ret->transcript = row[6];
-ret->geneId = row[7];
-}
-
-struct gencodeIntron *gencodeIntronLoad(char **row)
-/* Load a gencodeIntron from row fetched with select * from gencodeIntron
- * from database.  Dispose of this with gencodeIntronFree(). */
-{
-struct gencodeIntron *ret;
-
-AllocVar(ret);
-ret->chrom = cloneString(row[0]);
-ret->chromStart = sqlUnsigned(row[1]);
-ret->chromEnd = sqlUnsigned(row[2]);
-ret->name = cloneString(row[3]);
-ret->status = cloneString(row[4]);
-strcpy(ret->strand, row[5]);
-ret->transcript = cloneString(row[6]);
-ret->geneId = cloneString(row[7]);
-return ret;
-}
-
-struct gencodeIntron *gencodeIntronLoadAll(char *fileName) 
-/* Load all gencodeIntron from a whitespace-separated file.
- * Dispose of this with gencodeIntronFreeList(). */
-{
-struct gencodeIntron *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[8];
-
-while (lineFileRow(lf, row))
-    {
-    el = gencodeIntronLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct gencodeIntron *gencodeIntronLoadAllByChar(char *fileName, char chopper) 
-/* Load all gencodeIntron from a chopper separated file.
- * Dispose of this with gencodeIntronFreeList(). */
-{
-struct gencodeIntron *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[8];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = gencodeIntronLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct gencodeIntron *gencodeIntronLoadByQuery(struct sqlConnection *conn, char *query, int rowOffset)
-/* Load all gencodeIntron from table that satisfy the query given.  
- * Where query is of the form 'select * from example where something=something'
- * or 'select example.* from example, anotherTable where example.something = 
- * anotherTable.something'.
- * Dispose of this with gencodeIntronFreeList(). */
-{
-struct gencodeIntron *list = NULL, *el;
-struct sqlResult *sr;
-char **row;
-
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    el = gencodeIntronLoad(row+rowOffset);
-    slAddHead(&list, el);
-    }
-slReverse(&list);
-sqlFreeResult(&sr);
-return list;
-}
-
-void gencodeIntronSaveToDb(struct sqlConnection *conn, struct gencodeIntron *el, char *tableName, int updateSize)
-/* Save gencodeIntron as a row to the table specified by tableName. 
- * As blob fields may be arbitrary size updateSize specifies the approx size
- * of a string that would contain the entire query. Arrays of native types are
- * converted to comma separated strings and loaded as such, User defined types are
- * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
-{
-struct dyString *update = newDyString(updateSize);
-sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s','%s','%s','%s','%s')", 
-	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->status,  el->strand,  el->transcript,  el->geneId);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-}
-
-
-struct gencodeIntron *gencodeIntronCommaIn(char **pS, struct gencodeIntron *ret)
-/* Create a gencodeIntron out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new gencodeIntron */
-{
-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->status = sqlStringComma(&s);
-sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
-ret->transcript = sqlStringComma(&s);
-ret->geneId = sqlStringComma(&s);
-*pS = s;
-return ret;
-}
-
-void gencodeIntronFree(struct gencodeIntron **pEl)
-/* Free a single dynamically allocated gencodeIntron such as created
- * with gencodeIntronLoad(). */
-{
-struct gencodeIntron *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->chrom);
-freeMem(el->name);
-freeMem(el->status);
-freeMem(el->transcript);
-freeMem(el->geneId);
-freez(pEl);
-}
-
-void gencodeIntronFreeList(struct gencodeIntron **pList)
-/* Free a list of dynamically allocated gencodeIntron's */
-{
-struct gencodeIntron *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    gencodeIntronFree(&el);
-    }
-*pList = NULL;
-}
-
-void gencodeIntronOutput(struct gencodeIntron *el, FILE *f, char sep, char lastSep) 
-/* Print out gencodeIntron.  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);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->status);
-if (sep == ',') fputc('"',f);
-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->transcript);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->geneId);
-if (sep == ',') fputc('"',f);
-fputc(lastSep,f);
-}
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */
-
-void gencodeIntronTableCreate(struct sqlConnection *conn, char *tableName, int indexSize)
-/* Create a gencodeIntron table with the given name */
-{
-char *createString =
-"CREATE TABLE %s (\n"
-"       chrom varchar(255) not null,	# Chromosome\n"
-"       chromStart int unsigned not null,	# Start position in chromosome\n"
-"       chromEnd int unsigned not null,	# End position in chromosome\n"
-"       name varchar(255) not null,	# Intron ID\n"
-"       status enum('not_tested', 'RT_positive','RT_negative','RT_wrong_junction','RT_submitted', 'RACE_validated'),      # Status\n"
-"       strand char(1) not null,	# + or -\n"
-"       transcript varchar(255) not null,	# Transcript ID from GTF\n"
-"       geneId varchar(255) not null,	# Gene ID from GTF\n"
-"    INDEX(chrom(%d),chromStart),\n"
-"    INDEX(chrom(%d),chromEnd)\n"
-")\n";
-struct dyString *dy = newDyString(1024);
-sqlDyStringPrintf(dy, createString, tableName, indexSize, indexSize, indexSize);
-sqlRemakeTable(conn, tableName, dy->string);
-dyStringFree(&dy);
-}
-