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/orthoMap/mgcFastaForBed.c src/hg/orthoMap/mgcFastaForBed.c
index a931093..b5dbd2d 100644
--- src/hg/orthoMap/mgcFastaForBed.c
+++ src/hg/orthoMap/mgcFastaForBed.c
@@ -1,67 +1,67 @@
 /* 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 "hdb.h"
 #include "bed.h"
 #include "dnaseq.h"
 #include "fa.h"
 #include "dnautil.h"
 
 void usage()
 {
 errAbort("mgcFastaForBed - Take a bed file and return a fasta file\n"
 	 "with exons uppercase and introns lowercase.\n"
 	 "usage:\n"
 	 "   mgcFastaForBed db bedName fastaOutName\n");
 }
 
 struct dnaSeq *seqFromBed(char *db, struct bed *bed)
 /* Allocate a dnaSeq and uppercase the parts that are covered by the bed. 
  Free with dnaSeqFree().*/
 {
 struct dnaSeq *seq = hChromSeq(db, bed->chrom, bed->chromStart, bed->chromEnd);
 int i=0,j=0;
 for(i=0;i<bed->blockCount; i++)
     {
     int start = bed->chromStarts[i];
     int end = bed->chromStarts[i] + bed->blockSizes[i];
     for(j=start; j<end; j++)
 	seq->dna[j] = toupper(seq->dna[j]);
     }
 if(sameWord(bed->strand, "-"))
     reverseComplement(seq->dna, seq->size);
 return seq;
 }
 
 void mgcFastaForBeds(char *db, struct bed *bedList, FILE *out)
 /* Convert beds to sequence and output. */
 {
 struct bed *bed = NULL;
 char nameBuff[1024];
 warn("Converting beds");
 for(bed = bedList; bed != NULL; bed = bed->next)
     {
     struct dnaSeq *seq = seqFromBed(db, bed);
     safef(nameBuff, sizeof(nameBuff), "%s-%s:%d-%d-%s", bed->name, bed->chrom, 
 	  bed->chromStart, bed->chromEnd, bed->strand);
     faWriteNext(out, nameBuff, seq->dna, seq->size);
     dnaSeqFree(&seq);
     }
 }
 
 int main(int argc, char *argv[])
 {
 struct bed *bedList = NULL;
 FILE *out = NULL;
 if(argc != 4)
     usage();
 char *db = argv[1];
 warn("Loading Beds.");
 bedList = bedLoadAll(argv[2]);
 out = mustOpen(argv[3], "w");
 dnaUtilOpen();
 mgcFastaForBeds(db, bedList, out);
 warn("Done");
 return 0;
 }