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/cgapSage/cgapSage.c src/hg/lib/cgapSage/cgapSage.c
index 2fc4310..616c11a 100644
--- src/hg/lib/cgapSage/cgapSage.c
+++ src/hg/lib/cgapSage/cgapSage.c
@@ -1,281 +1,281 @@
 /* cgapSage.c was originally generated by the autoSql program, which also 
  * generated cgapSage.h and cgapSage.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 "cgapSage/cgapSage.h"
 
 
 struct cgapSage *cgapSageLoad(char **row)
 /* Load a cgapSage from row fetched with select * from cgapSage
  * from database.  Dispose of this with cgapSageFree(). */
 {
 struct cgapSage *ret;
 
 AllocVar(ret);
 ret->numLibs = sqlUnsigned(row[8]);
 ret->numSnps = sqlUnsigned(row[12]);
 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]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
 {
 int sizeOne;
 sqlUnsignedDynamicArray(row[9], &ret->libIds, &sizeOne);
 assert(sizeOne == ret->numLibs);
 }
 {
 int sizeOne;
 sqlUnsignedDynamicArray(row[10], &ret->freqs, &sizeOne);
 assert(sizeOne == ret->numLibs);
 }
 {
 int sizeOne;
 sqlDoubleDynamicArray(row[11], &ret->tagTpms, &sizeOne);
 assert(sizeOne == ret->numLibs);
 }
 {
 int sizeOne;
 sqlStringDynamicArray(row[13], &ret->snps, &sizeOne);
 assert(sizeOne == ret->numSnps);
 }
 return ret;
 }
 
 struct cgapSage *cgapSageLoadAll(char *fileName) 
 /* Load all cgapSage from a whitespace-separated file.
  * Dispose of this with cgapSageFreeList(). */
 {
 struct cgapSage *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[14];
 
 while (lineFileRow(lf, row))
     {
     el = cgapSageLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct cgapSage *cgapSageLoadAllByChar(char *fileName, char chopper) 
 /* Load all cgapSage from a chopper separated file.
  * Dispose of this with cgapSageFreeList(). */
 {
 struct cgapSage *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[14];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = cgapSageLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct cgapSage *cgapSageCommaIn(char **pS, struct cgapSage *ret)
 /* Create a cgapSage out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new cgapSage */
 {
 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->numLibs = sqlUnsignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->libIds, ret->numLibs);
 for (i=0; i<ret->numLibs; ++i)
     {
     ret->libIds[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->freqs, ret->numLibs);
 for (i=0; i<ret->numLibs; ++i)
     {
     ret->freqs[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->tagTpms, ret->numLibs);
 for (i=0; i<ret->numLibs; ++i)
     {
     ret->tagTpms[i] = sqlDoubleComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->numSnps = sqlUnsignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->snps, ret->numSnps);
 for (i=0; i<ret->numSnps; ++i)
     {
     ret->snps[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 *pS = s;
 return ret;
 }
 
 void cgapSageFree(struct cgapSage **pEl)
 /* Free a single dynamically allocated cgapSage such as created
  * with cgapSageLoad(). */
 {
 struct cgapSage *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->libIds);
 freeMem(el->freqs);
 freeMem(el->tagTpms);
 /* All strings in snps are allocated at once, so only need to free first. */
 if (el->snps != NULL)
     freeMem(el->snps[0]);
 freeMem(el->snps);
 freez(pEl);
 }
 
 void cgapSageFreeList(struct cgapSage **pList)
 /* Free a list of dynamically allocated cgapSage's */
 {
 struct cgapSage *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     cgapSageFree(&el);
     }
 *pList = NULL;
 }
 
 void cgapSageOutput(struct cgapSage *el, FILE *f, char sep, char lastSep) 
 /* Print out cgapSage.  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->numLibs);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->numLibs; ++i)
     {
     fprintf(f, "%u", el->libIds[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->numLibs; ++i)
     {
     fprintf(f, "%u", el->freqs[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->numLibs; ++i)
     {
     fprintf(f, "%g", el->tagTpms[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 fprintf(f, "%u", el->numSnps);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->numSnps; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->snps[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 int cgapSageCmp(const void *va, const void *vb)
 /* Compare based on chrom,start,name. */
 {
 const struct cgapSage *a = *((struct cgapSage **)va);
 const struct cgapSage *b = *((struct cgapSage **)vb);
 int dif;
 dif = strcmp(a->chrom, b->chrom);
 if (dif == 0)
     dif = a->chromStart - b->chromStart;
 if (dif == 0)
     dif = strcmp(a->name, b->name);
 return dif;
 }