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/encode/encodeIndels.c src/hg/lib/encode/encodeIndels.c
index b229b62..6b62acf 100644
--- src/hg/lib/encode/encodeIndels.c
+++ src/hg/lib/encode/encodeIndels.c
@@ -1,207 +1,207 @@
 /* encodeIndels.c was originally generated by the autoSql program, which also 
  * generated encodeIndels.h and encodeIndels.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2011 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 "encode/encodeIndels.h"
 
 
 void encodeIndelsStaticLoad(char **row, struct encodeIndels *ret)
 /* Load a row from encodeIndels 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->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
 ret->reserved = sqlUnsigned(row[8]);
 ret->traceName = row[9];
 ret->traceId = row[10];
 ret->tracePos = sqlUnsigned(row[11]);
 strcpy(ret->traceStrand, row[12]);
 ret->variant = row[13];
 ret->reference = row[14];
 }
 
 struct encodeIndels *encodeIndelsLoad(char **row)
 /* Load a encodeIndels from row fetched with select * from encodeIndels
  * from database.  Dispose of this with encodeIndelsFree(). */
 {
 struct encodeIndels *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->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
 ret->reserved = sqlUnsigned(row[8]);
 ret->traceName = cloneString(row[9]);
 ret->traceId = cloneString(row[10]);
 ret->tracePos = sqlUnsigned(row[11]);
 strcpy(ret->traceStrand, row[12]);
 ret->variant = cloneString(row[13]);
 ret->reference = cloneString(row[14]);
 return ret;
 }
 
 struct encodeIndels *encodeIndelsLoadAll(char *fileName) 
 /* Load all encodeIndels from a whitespace-separated file.
  * Dispose of this with encodeIndelsFreeList(). */
 {
 struct encodeIndels *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[15];
 
 while (lineFileRow(lf, row))
     {
     el = encodeIndelsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct encodeIndels *encodeIndelsLoadAllByChar(char *fileName, char chopper) 
 /* Load all encodeIndels from a chopper separated file.
  * Dispose of this with encodeIndelsFreeList(). */
 {
 struct encodeIndels *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[15];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = encodeIndelsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct encodeIndels *encodeIndelsCommaIn(char **pS, struct encodeIndels *ret)
 /* Create a encodeIndels out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new encodeIndels */
 {
 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->thickStart = sqlUnsignedComma(&s);
 ret->thickEnd = sqlUnsignedComma(&s);
 ret->reserved = sqlUnsignedComma(&s);
 ret->traceName = sqlStringComma(&s);
 ret->traceId = sqlStringComma(&s);
 ret->tracePos = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->traceStrand, sizeof(ret->traceStrand));
 ret->variant = sqlStringComma(&s);
 ret->reference = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void encodeIndelsFree(struct encodeIndels **pEl)
 /* Free a single dynamically allocated encodeIndels such as created
  * with encodeIndelsLoad(). */
 {
 struct encodeIndels *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->traceName);
 freeMem(el->traceId);
 freeMem(el->variant);
 freeMem(el->reference);
 freez(pEl);
 }
 
 void encodeIndelsFreeList(struct encodeIndels **pList)
 /* Free a list of dynamically allocated encodeIndels's */
 {
 struct encodeIndels *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     encodeIndelsFree(&el);
     }
 *pList = NULL;
 }
 
 void encodeIndelsOutput(struct encodeIndels *el, FILE *f, char sep, char lastSep) 
 /* Print out encodeIndels.  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);
 fprintf(f, "%u", el->thickStart);
 fputc(sep,f);
 fprintf(f, "%u", el->thickEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->reserved);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->traceName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->traceId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->tracePos);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->traceStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->variant);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->reference);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */