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/lib/annoAssembly.c src/lib/annoAssembly.c
index 1f74c8e..df7ab4d 100644
--- src/lib/annoAssembly.c
+++ src/lib/annoAssembly.c
@@ -1,77 +1,77 @@
 /* annoAssembly -- basic metadata about an assembly for the annoGrator framework. */
 
 /* Copyright (C) 2013 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 "annoAssembly.h"
 #include "dnaseq.h"
 #include "obscure.h"
 #include "twoBit.h"
 
 struct annoAssembly *annoAssemblyNew(char *name, char *twoBitPath)
 /* Return an annoAssembly with open twoBitFile. */
 {
 struct annoAssembly *aa;
 AllocVar(aa);
 aa->name = cloneString(name);
 aa->twoBitPath = cloneString(twoBitPath);
 aa->tbf = twoBitOpen(aa->twoBitPath);
 aa->curSeq = NULL;
 return aa;
 }
 
 struct slName *annoAssemblySeqNames(struct annoAssembly *aa)
 /* Return a list of sequence names in this assembly. */
 {
 struct slName *seqNames = twoBitSeqNames(aa->twoBitPath);
 slSort(&seqNames, slNameCmp);
 return seqNames;
 }
 
 uint annoAssemblySeqSize(struct annoAssembly *aa, char *seqName)
 /* Return the number of bases in seq which must be in aa's twoBitFile. */
 {
 if (aa->seqSizes == NULL)
     aa->seqSizes = hashNew(digitsBaseTwo(aa->tbf->seqCount));
 struct hashEl *hel = hashLookup(aa->seqSizes, seqName);
 uint seqSize;
 if (hel != NULL)
     seqSize = (uint)(hel->val - NULL);
 else
     {
     seqSize = (uint)twoBitSeqSize(aa->tbf, seqName);
     char *pt = NULL;
     hashAdd(aa->seqSizes, seqName, pt + seqSize);
     }
 return seqSize;
 }
 
 void annoAssemblyGetSeq(struct annoAssembly *aa, char *seqName, uint start, uint end,
 			char *buf, size_t bufSize)
 /* Copy sequence to buf; bufSize must be at least end-start+1 chars in length. */
 {
 if (aa->curSeq == NULL || differentString(aa->curSeq->name, seqName))
     {
     dnaSeqFree(&aa->curSeq);
     aa->curSeq = twoBitReadSeqFragLower(aa->tbf, seqName, 0, 0);
     }
 uint chromSize = aa->curSeq->size;
 if (end > chromSize || start > chromSize || start > end)
     errAbort("annoAssemblyGetSeq: bad coords [%u,%u) (sequence %s size %u)",
 	     start, end, seqName, chromSize);
 safencpy(buf, bufSize, aa->curSeq->dna+start, end-start);
 }
 
 void annoAssemblyClose(struct annoAssembly **pAa)
 /* Close aa's twoBitFile and free mem. */
 {
 if (*pAa == NULL)
     return;
 struct annoAssembly *aa = *pAa;
 freeMem(aa->name);
 freeMem(aa->twoBitPath);
 twoBitClose(&(aa->tbf));
 hashFree(&(aa->seqSizes));
 freez(pAa);
 }