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/snp125.c src/hg/lib/snp125.c
deleted file mode 100644
index accf9e7..0000000
--- src/hg/lib/snp125.c
+++ /dev/null
@@ -1,324 +0,0 @@
-/* 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;
-}
-