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/intronSizes/intronSizes.c src/hg/intronSizes/intronSizes.c
index fb387dc..bfa1079 100644
--- src/hg/intronSizes/intronSizes.c
+++ src/hg/intronSizes/intronSizes.c
@@ -1,102 +1,102 @@
 /* intronSizes - Output list of intron sizes.. */
 
 /* 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 "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "hash.h"
 #include "cheapcgi.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "genePred.h"
 
 
 char *chromName;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "intronSizes - Output list of intron sizes.\n" 
   "usage:\n"
   "   intronSizes database geneTable\n"
   "options:\n"
   "   -chrom=chrN - restrict to a particular chromosome\n"
   "   -withUtr - restrict to genes with UTR regions\n"
   );
 }
 
 void genePredIntrons(struct genePred *gp, struct bed **bedList)
 /* get list of introns (bed format) for a genePred */
 /* append list of introns to bedList */
 {
 int exonIx=1;
 struct bed *bed = NULL;
 
 for (exonIx=1; exonIx < gp->exonCount; ++exonIx)
     {
     int intronStart = gp->exonEnds[exonIx-1];
     int intronEnd = gp->exonStarts[exonIx];
     if (intronEnd > intronStart)
         {
         AllocVar(bed);
         bed->chrom = cloneString(gp->chrom);
         bed->chromStart = intronStart;
         bed->chromEnd = intronEnd;
         bed->name = cloneString(gp->name);
         bed->score = intronEnd-intronStart;
         bed->strand[0] = gp->strand[0];
         bed->strand[1] = gp->strand[1];
         slAddHead(bedList, bed);
         }
     }
 }
 
 void intronSizes(char *database, char *table)
 /* intronSizes - Output list of intron sizes.. */
 {
 struct dyString *query = newDyString(1024);
 struct sqlConnection *conn;
 struct sqlResult *sr;
 char **row;
 struct genePred *gp;
 int rowOffset;
 struct bed *bedList = NULL, *bed = NULL;
 
 hSetDb(database);
 rowOffset = hOffsetPastBin(NULL, table);
 conn = hAllocConn(database);
 sqlDyStringPrintf(query, "select * from %s", table);
 if (chromName != NULL)
     dyStringPrintf(query, " where chrom = '%s'", chromName);
 if (cgiBoolean("withUtr"))
     {
     dyStringPrintf(query, " %s txStart != cdsStart", 
         (chromName == NULL ? "where" : "and"));
     }
 sr = sqlGetResult(conn, query->string);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     gp = genePredLoad(row+rowOffset);
     genePredIntrons(gp, &bedList);
     slReverse(&bedList);
     for (bed = bedList ; bed != NULL ; bed=bed->next)
         bedTabOutN(bed,6, stdout);
     bedFreeList(&bedList);
     genePredFree(&gp);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 cgiSpoof(&argc, argv);
 chromName = cgiOptionalString("chrom");
 if (argc != 3)
     usage();
 intronSizes(argv[1], argv[2]);
 return 0;
 }