4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/lib/snp.c src/hg/lib/snp.c
index 7545da5..f1f50f1 100644
--- src/hg/lib/snp.c
+++ src/hg/lib/snp.c
@@ -1,259 +1,259 @@
 /* snp.c was originally generated by the autoSql program, which also 
  * generated snp.h and snp.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. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "snp.h"
 
 
 void snpStaticLoad(char **row, struct snp *ret)
 /* Load a row from snp 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->observed = row[6];
 ret->molType = row[7];
 ret->class = row[8];
 ret->valid = row[9];
 ret->avHet = atof(row[10]);
 ret->avHetSE = atof(row[11]);
 ret->func = row[12];
 ret->locType = row[13];
 ret->source = row[14];
 ret->exception = row[15];
 }
 
 struct snp *snpLoad(char **row)
 /* Load a snp from row fetched with select * from snp
  * from database.  Dispose of this with snpFree(). */
 {
 struct snp *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->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->source = cloneString(row[14]);
 ret->exception = cloneString(row[15]);
 return ret;
 }
 
 struct snp *snpLoadAll(char *fileName) 
 /* Load all snp from a whitespace-separated file.
  * Dispose of this with snpFreeList(). */
 {
 struct snp *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[16];
 
 while (lineFileRow(lf, row))
     {
     el = snpLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snp *snpLoadAllByChar(char *fileName, char chopper) 
 /* Load all snp from a chopper separated file.
  * Dispose of this with snpFreeList(). */
 {
 struct snp *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[16];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = snpLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snp *snpLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all snp 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 snpFreeList(). */
 {
 struct snp *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = snpLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void snpSaveToDb(struct sqlConnection *conn, struct snp *el, char *tableName, int updateSize)
 /* Save snp 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',%u,'%s','%s','%s','%s','%s',%g,%g,'%s','%s','%s','%s')", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->observed,  el->molType,  el->class,  el->valid,  el->avHet,  el->avHetSE,  el->func,  el->locType,  el->source,  el->exception);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct snp *snpCommaIn(char **pS, struct snp *ret)
 /* Create a snp out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new snp */
 {
 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->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->source = sqlStringComma(&s);
 ret->exception = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void snpFree(struct snp **pEl)
 /* Free a single dynamically allocated snp such as created
  * with snpLoad(). */
 {
 struct snp *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->observed);
 freeMem(el->molType);
 freeMem(el->class);
 freeMem(el->valid);
 freeMem(el->func);
 freeMem(el->locType);
 freeMem(el->source);
 freeMem(el->exception);
 freez(pEl);
 }
 
 void snpFreeList(struct snp **pList)
 /* Free a list of dynamically allocated snp's */
 {
 struct snp *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     snpFree(&el);
     }
 *pList = NULL;
 }
 
 void snpOutput(struct snp *el, FILE *f, char sep, char lastSep) 
 /* Print out snp.  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->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);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->source);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->exception);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */