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/gencodeIntron.c src/hg/cgilib/gencodeIntron.c
new file mode 100644
index 0000000..34ba349
--- /dev/null
+++ src/hg/cgilib/gencodeIntron.c
@@ -0,0 +1,226 @@
+/* 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);
+}
+