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/snp125.c src/hg/cgilib/snp125.c
new file mode 100644
index 0000000..accf9e7
--- /dev/null
+++ src/hg/cgilib/snp125.c
@@ -0,0 +1,324 @@
+/* snp125.c was originally generated by the autoSql program, which also 
+ * generated snp125.h and snp125.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 "snp125.h"
+
+
+void snp125StaticLoad(char **row, struct snp125 *ret)
+/* Load a row from snp125 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]);
+ret->strand = row[5];
+ret->refNCBI = row[6];
+ret->refUCSC = row[7];
+ret->observed = row[8];
+ret->molType = row[9];
+ret->class = row[10];
+ret->valid = row[11];
+ret->avHet = atof(row[12]);
+ret->avHetSE = atof(row[13]);
+ret->func = row[14];
+ret->locType = row[15];
+ret->weight = sqlUnsigned(row[16]);
+}
+
+struct snp125 *snp125Load(char **row)
+/* Load a snp125 from row fetched with select * from snp125
+ * from database.  Dispose of this with snp125Free(). */
+{
+struct snp125 *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]);
+ret->strand = cloneString(row[5]);
+ret->refNCBI = cloneString(row[6]);
+ret->refUCSC = cloneString(row[7]);
+ret->observed = cloneString(row[8]);
+ret->molType = cloneString(row[9]);
+ret->class = cloneString(row[10]);
+ret->valid = cloneString(row[11]);
+ret->avHet = atof(row[12]);
+ret->avHetSE = atof(row[13]);
+ret->func = cloneString(row[14]);
+ret->locType = cloneString(row[15]);
+ret->weight = sqlUnsigned(row[16]);
+return ret;
+}
+
+struct snp125 *snp125LoadAll(char *fileName) 
+/* Load all snp125 from a whitespace-separated file.
+ * Dispose of this with snp125FreeList(). */
+{
+struct snp125 *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[17];
+
+while (lineFileRow(lf, row))
+    {
+    el = snp125Load(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct snp125 *snp125LoadAllByChar(char *fileName, char chopper) 
+/* Load all snp125 from a chopper separated file.
+ * Dispose of this with snp125FreeList(). */
+{
+struct snp125 *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[17];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = snp125Load(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct snp125 *snp125CommaIn(char **pS, struct snp125 *ret)
+/* Create a snp125 out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new snp125 */
+{
+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);
+ret->strand = sqlStringComma(&s);
+ret->refNCBI = sqlStringComma(&s);
+ret->refUCSC = sqlStringComma(&s);
+ret->observed = sqlStringComma(&s);
+ret->molType = sqlStringComma(&s);
+ret->class = sqlStringComma(&s);
+ret->valid = sqlStringComma(&s);
+ret->avHet = sqlFloatComma(&s);
+ret->avHetSE = sqlFloatComma(&s);
+ret->func = sqlStringComma(&s);
+ret->locType = sqlStringComma(&s);
+ret->weight = sqlUnsignedComma(&s);
+*pS = s;
+return ret;
+}
+
+void snp125Free(struct snp125 **pEl)
+/* Free a single dynamically allocated snp125 such as created
+ * with snp125Load(). */
+{
+struct snp125 *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->strand);
+freeMem(el->refNCBI);
+freeMem(el->refUCSC);
+freeMem(el->observed);
+freeMem(el->molType);
+freeMem(el->class);
+freeMem(el->valid);
+freeMem(el->func);
+freeMem(el->locType);
+freez(pEl);
+}
+
+void snp125FreeList(struct snp125 **pList)
+/* Free a list of dynamically allocated snp125's */
+{
+struct snp125 *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    snp125Free(&el);
+    }
+*pList = NULL;
+}
+
+void snp125Output(struct snp125 *el, FILE *f, char sep, char lastSep) 
+/* Print out snp125.  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->refNCBI);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->refUCSC);
+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->molType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->class);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->valid);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%g", el->avHet);
+fputc(sep,f);
+fprintf(f, "%g", el->avHetSE);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->func);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->locType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->weight);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+
+void snp125TableCreate(struct sqlConnection *conn, char *tableName)
+/* create a snp125 table */
+{
+char *createString =
+"CREATE TABLE %s (\n"
+"    bin           smallint(5) unsigned not null,\n"
+"    chrom         varchar(15) not null,\n"
+"    chromStart    int(10) unsigned not null,\n"
+"    chromEnd      int(10) unsigned not null,\n"
+"    name          varchar(15) not null,\n"
+"    score         smallint(5) unsigned not null,\n"
+"    strand        enum('?','+','-') default '?' not null,\n"
+"    refNCBI       blob not null,\n"
+"    refUCSC       blob not null,\n"
+"    observed      varchar(255) not null,\n"
+"    molType       enum('unknown', 'genomic', 'cDNA') DEFAULT 'unknown' not null,\n"
+"    class         enum('unknown', 'single', 'in-del', 'het', 'microsatellite',"
+"                  'named', 'no var', 'mixed', 'mnp', 'insertion', 'deletion') \n"
+"                  DEFAULT 'unknown' NOT NULL,\n"
+"    valid         set('unknown', 'by-frequency', 'by-cluster', 'by-submitter', \n"
+"                  'by-2hit-2allele', 'by-hapmap') \n"
+"                  DEFAULT 'unknown' NOT NULL,\n"
+"    avHet 	   float not null,\n"
+"    avHetSE 	   float not null,\n"
+"    func          set( 'unknown', 'locus', 'coding', 'coding-synon', 'coding-nonsynon', \n"
+"                  'untranslated', 'intron','splice-site', 'cds-reference') \n"
+"                  DEFAULT 'unknown' NOT NULL,\n"
+"    locType       enum ('unknown', 'range', 'exact', 'between',\n"
+"                  'rangeInsertion', 'rangeSubstitution', 'rangeDeletion') DEFAULT 'unknown' NOT NULL\n,"
+"    weight        int not null\n"
+")\n";
+
+struct dyString *dy = newDyString(1024);
+sqlDyStringPrintf(dy, createString, tableName);
+sqlRemakeTable(conn, tableName, dy->string);
+dyStringFree(&dy);
+}
+
+int snp125Cmp(const void *va, const void *vb)
+{
+const struct snp125 *a = *((struct snp125 **)va);
+const struct snp125 *b = *((struct snp125 **)vb);
+int dif;
+dif = strcmp(a->chrom, b->chrom);
+if (dif == 0)
+    dif = a->chromStart - b->chromStart;
+return dif;
+}
+
+
+/*  Additional function for extended processing */
+
+
+struct snp125Extended *snpExtendedLoad(char **row)
+/* Load a snp125 from row fetched with select * from snp125
+ * from database.  Additional fields are for run-time calculations */
+{
+struct snp125Extended *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]);
+ret->strand = cloneString(row[5]);
+ret->observed = cloneString(row[6]);
+ret->molType = cloneString(row[7]);
+ret->class = cloneString(row[8]);
+ret->valid = cloneString(row[9]);
+ret->avHet = atof(row[10]);
+ret->avHetSE = atof(row[11]);
+ret->func = cloneString(row[12]);
+ret->locType = cloneString(row[13]);
+ret->refNCBI = NULL;
+ret->refUCSC = NULL;
+ret->weight = 0;
+ret->nameExtra = cloneString("");
+ret->color = 0;
+
+return ret;
+}
+
+int snpVersion(char *track)
+/* If track starts with snpNNN where NNN is 125 or later, return the number;
+ * otherwise return 0. */
+{
+int version = 0;
+if ( startsWith("snp", track) && strlen(track) >= 6 &&
+     isdigit(track[3]) && isdigit(track[4]) && isdigit(track[5]) &&
+     atoi(track+3) >= 125 )
+    version = atoi(track+3);
+return version;
+}
+