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/qaAgpToQacIdx/qaAgpToQacIdx.c src/hg/qaAgpToQacIdx/qaAgpToQacIdx.c
index 6abbdf3..ffbd285 100644
--- src/hg/qaAgpToQacIdx/qaAgpToQacIdx.c
+++ src/hg/qaAgpToQacIdx/qaAgpToQacIdx.c
@@ -1,116 +1,116 @@
 /* qaAgpToQacIdx - build compressed quality file and index file. */
 
 /* Copyright (C) 2007 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 "hash.h"
 #include "options.h"
 #include "agp.h"
 #include "agpFrag.h"
 #include "agpGap.h"
 #include "qaSeq.h"
 
 #define FAKE_GAP_QUAL 100
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "qaAgpToQacIdx - Build compressed quality file and corresponding index file\n"
   "usage:\n"
   "   qaAgpToQacIdx in.agp in.qa out.qac out.qdx\n"
   );
 }
 
 void qaAgpToQacIdx(char *inAgp, char *inQa, char *outQac, char *outQdx)
 /* qaAgpToQacIdx - build compressed quality file and index file. */
 {
 struct hash *agpLists = agpLoadAll(inAgp);
 struct qaSeq *qa, *qaList = NULL;
 struct lineFile *qalf = lineFileOpen(inQa, TRUE);
 int seq_count = 0;
 char *s;
 char buffer[1024];
 struct hashEl *hel;
 struct agp *agp;
 struct agpGap *gap;
 FILE *qacf = mustOpen(outQac, "wb");
 FILE *qdxf = mustOpen(outQdx, "wb");
 off_t offset;
 
 /* Add gap data to the qa */
 while ((qa = qaReadNext(qalf)) != NULL)
 	{
 	seq_count++;
 
 	/* only keep first word */
 	if ((s = strchr(qa->name, ' ')) != NULL)
 		{
 		*s = '\0';
 		}
 	
 	safef(buffer, sizeof(buffer), "%s", qa->name);
 
 	/* strip off anything after the first '.' */
 	/* scaffold_0.1-193456 seemed redundant,  */
 	/* and doesn't match the agp file         */
 	if ((s = strchr(buffer, '.')) != NULL)
 		{
 		*s = '\0';
 		}
 
 	/* set fake quality values for gaps */
 	if ((hel = hashLookup(agpLists, buffer)) != NULL)
 		{
 		for (agp = (struct agp *) hel->val; agp != NULL; agp = agp->next)
 			{
 			if (! agp->isFrag)
 				{
 				gap = (struct agpGap *) (agp->entry);
 				if (qa->size - gap->chromStart + 1 > gap->size)
 					{
 					memset(qa->qa + gap->chromStart - 1, FAKE_GAP_QUAL, gap->size);
 					}
 				else
 					{
 					errAbort("gap too big: chromStart = %d size = %d\n", gap->chromStart, gap->size);
 					}
 				}
 			}
 		}
 
 	slAddHead(&qaList, qa);
 	}
 
 lineFileClose(&qalf);
 agpHashFree(&agpLists);
 
 
 /* Write our the qac and index */
 qacWriteHead(qacf);
 fprintf(qdxf, "%d\n", seq_count);
 for (qa = qaList; qa != NULL; qa = qa->next)
 	{
 	if ((offset = ftello(qacf)) == (off_t) -1)
 		{
 		errAbort("ftello() failed\n");
 		}
 	fprintf(qdxf, "%s\t%ld\n", qa->name, offset);
 	qacWriteNext(qacf, qa);
 	}
 
 /* Clean up after ourselves */
 carefulClose(&qacf);
 carefulClose(&qdxf);
 qaSeqFreeList(&qaList);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc != 5)
 	usage();
 qaAgpToQacIdx(argv[1], argv[2], argv[3], argv[4]);
 return EXIT_SUCCESS;
 }