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/encode/ldGencodeIntron/ldGencodeIntron.c src/hg/encode/ldGencodeIntron/ldGencodeIntron.c
index cf077b7..1b64dcf 100644
--- src/hg/encode/ldGencodeIntron/ldGencodeIntron.c
+++ src/hg/encode/ldGencodeIntron/ldGencodeIntron.c
@@ -1,85 +1,85 @@
 /* ldGencodeIntron - load intron id's and status from Gencode project GTF file */
 
 /* 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 "jksql.h"
 #include "hdb.h"
 #include "bed.h"
 #include "gff.h"
 #include "hgRelate.h"
 #include "gencodeIntron.h"
 #include "options.h"
 
 
 void usage()
 {
 errAbort(
        "ldGencodeIntron - load intron table from a Gencode gtf file.\n"
        "usage:\n"
        "     ldGencodeIntron database table file(s).gtf\n");
 }
 
 struct optionSpec options[] = {{NULL, 0}};
 
 void ldGencodeIntron(char *database, char *table,  
                         int gtfCount, char *gtfNames[])
 /* Load Gencode intron status table from GTF files with
  * intron_id and intron_status keywords */
 {
 struct gffFile *gff, *gffList = NULL;
 struct gffLine *gffLine;
 struct gencodeIntron *intron, *intronList = NULL;
 struct sqlConnection *conn;
 FILE *f;
 int i;
 int introns = 0;
 
 for (i=0; i<gtfCount; i++)
     {
     verbose(1, "Reading %s\n", gtfNames[i]);
     gff = gffRead(gtfNames[i]);
     for (gffLine = gff->lineList; gffLine != NULL; gffLine = gffLine->next)
         {
         if (sameWord(gffLine->feature, "intron"))
             {
             AllocVar(intron);
             intron->chrom = gffLine->seq;
             intron->chromStart = gffLine->start;
             intron->chromEnd = gffLine->end;
             intron->name = gffLine->intronId;
             intron->strand[0] = gffLine->strand;
             intron->strand[1] = 0;
             intron->status = gffLine->intronStatus;
             intron->transcript = gffLine->group;
             intron->geneId = gffLine->geneId;
             slAddHead(&intronList, intron);
             verbose(2, "%s %s\n", intron->chrom, intron->name);
             introns++;
             }
         }
     }
 slSort(&intronList, bedCmp);
 f = hgCreateTabFile(".", table);
 for (intron = intronList; intron != NULL; intron = intron->next)
     gencodeIntronTabOut(intron, f);
 carefulClose(&f);
 
 verbose(1, "%d introns in %d files\n", introns, gtfCount);
 hSetDb(database);
 conn = sqlConnect(database);
 gencodeIntronTableCreate(conn, table, hGetMinIndexLength());
 hgLoadTabFile(conn, ".", table, &f);
 sqlDisconnect(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line */
 {
 optionInit(&argc, argv, options);
 if (argc < 3)
     usage();
 ldGencodeIntron(argv[1], argv[2], argc-3, argv+3);
 return 0;
 }