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/txPaper/txGeneBakeOff/refCluster.c src/hg/txPaper/txGeneBakeOff/refCluster.c
index 6144d51..f0879ef 100644
--- src/hg/txPaper/txGeneBakeOff/refCluster.c
+++ src/hg/txPaper/txGeneBakeOff/refCluster.c
@@ -1,168 +1,168 @@
 /* refCluster.c was originally generated by the autoSql program, which also 
  * generated refCluster.h and refCluster.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 "refCluster.h"
 
 
 struct refCluster *refClusterLoad(char **row)
 /* Load a refCluster from row fetched with select * from refCluster
  * from database.  Dispose of this with refClusterFree(). */
 {
 struct refCluster *ret;
 
 AllocVar(ret);
 ret->refCount = sqlSigned(row[5]);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlSigned(row[1]);
 ret->chromEnd = sqlSigned(row[2]);
 ret->name = cloneString(row[3]);
 safecpy(ret->strand, sizeof(ret->strand), row[4]);
 {
 int sizeOne;
 sqlStringDynamicArray(row[6], &ret->refArray, &sizeOne);
 assert(sizeOne == ret->refCount);
 }
 return ret;
 }
 
 struct refCluster *refClusterLoadAll(char *fileName) 
 /* Load all refCluster from a whitespace-separated file.
  * Dispose of this with refClusterFreeList(). */
 {
 struct refCluster *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileRow(lf, row))
     {
     el = refClusterLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct refCluster *refClusterLoadAllByChar(char *fileName, char chopper) 
 /* Load all refCluster from a chopper separated file.
  * Dispose of this with refClusterFreeList(). */
 {
 struct refCluster *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = refClusterLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct refCluster *refClusterCommaIn(char **pS, struct refCluster *ret)
 /* Create a refCluster out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new refCluster */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlSignedComma(&s);
 ret->chromEnd = sqlSignedComma(&s);
 ret->name = sqlStringComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->refCount = sqlSignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->refArray, ret->refCount);
 for (i=0; i<ret->refCount; ++i)
     {
     ret->refArray[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 *pS = s;
 return ret;
 }
 
 void refClusterFree(struct refCluster **pEl)
 /* Free a single dynamically allocated refCluster such as created
  * with refClusterLoad(). */
 {
 struct refCluster *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 /* All strings in refArray are allocated at once, so only need to free first. */
 if (el->refArray != NULL)
     freeMem(el->refArray[0]);
 freeMem(el->refArray);
 freez(pEl);
 }
 
 void refClusterFreeList(struct refCluster **pList)
 /* Free a list of dynamically allocated refCluster's */
 {
 struct refCluster *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     refClusterFree(&el);
     }
 *pList = NULL;
 }
 
 void refClusterOutput(struct refCluster *el, FILE *f, char sep, char lastSep) 
 /* Print out refCluster.  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, "%d", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%d", 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->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->refCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->refCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->refArray[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */