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/makeDb/hgLoadAxt/hgLoadAxt.c src/hg/makeDb/hgLoadAxt/hgLoadAxt.c
index 4fd67b5..8f284db 100644
--- src/hg/makeDb/hgLoadAxt/hgLoadAxt.c
+++ src/hg/makeDb/hgLoadAxt/hgLoadAxt.c
@@ -1,92 +1,92 @@
 /* hgLoadAxt - Load an axt file index into the database. */
 
 /* Copyright (C) 2008 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 "portable.h"
 #include "hdb.h"
 #include "hgRelate.h"
 #include "scoredRef.h"
 #include "axt.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgLoadAxt - Load an axt file index into the database\n"
   "usage:\n"
   "   hgLoadAxt database table\n"
   "The axt files need to already exist in chromosome coordinates\n"
   "in the directory /gbdb/database/table.\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 void hgLoadAxt(char *database, char *table)
 /* hgLoadAxt - Load a axt file index into the database. */
 {
 char extFileDir[512];
 struct fileInfo *fileList = NULL, *fileEl;
 struct sqlConnection *conn;
 long count = 0;
 FILE *f = hgCreateTabFile(".", table);
 
 safef(extFileDir, sizeof(extFileDir), "/gbdb/%s/%s", database, table);
 fileList = listDirX(extFileDir, "*.axt", TRUE);
 conn = hgStartUpdate(database);
 scoredRefTableCreate(conn, table, hGetMinIndexLength(database));
 if (fileList == NULL)
     errAbort("%s doesn't exist or doesn't have any axt files", extFileDir);
 for (fileEl = fileList; fileEl != NULL; fileEl = fileEl->next)
     {
     char *fileName = fileEl->name;
     struct lineFile *lf = lineFileOpen(fileName, TRUE);
     struct axt *axt;
     struct scoredRef mr;
     off_t offset = 0;
     HGID extId = hgAddToExtFile(fileName, conn);
 
     verbose(1, "Indexing and tabulating %s\n", fileName);
     while ((axt = axtReadWithPos(lf, &offset)) != NULL)
         {
 	double maxScore = 100, minScore = -100;
 	++count;
 	ZeroVar(&mr);
 	mr.chrom = axt->tName;
 	mr.chromStart = axt->tStart;
 	mr.chromEnd = axt->tEnd;
 	if (axt->tStrand == '-')
 	    reverseIntRange(&mr.chromStart, &mr.chromEnd, hChromSize(database, mr.chrom));
 	mr.extFile = extId;
 	mr.offset = offset;
 	mr.score = (double)axt->score/(axt->tEnd - axt->tStart);
 	mr.score = (mr.score-minScore)/(maxScore-minScore);
 	if (mr.score > 1.0) mr.score = 1.0;
 	if (mr.score < 0.0) mr.score = 0.0;
 	fprintf(f, "%u\t", hFindBin(mr.chromStart, mr.chromEnd));
 	scoredRefTabOut(&mr, f);
 	axtFree(&axt);
 	}
     }
 verbose(1, "Loading %s into database\n", table);
 hgLoadTabFile(conn, ".", table, &f);
 hgEndUpdate(&conn, "Add %ld axts in %d files from %s", count, slCount(fileList), extFileDir);
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 hgLoadAxt(argv[1], argv[2]);
 return 0;
 }