src/hg/orthoMap/bedToFrames.c 4898794edd81be5285ea6e544acbedeaeb31bf78

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/bedToFrames.c src/hg/orthoMap/bedToFrames.c
index 6b092e7..cc132d2 100644
--- src/hg/orthoMap/bedToFrames.c
+++ src/hg/orthoMap/bedToFrames.c
@@ -1,78 +1,78 @@
 /* bedToFrames.c Quick program to create a frame based version
    for browsing custom tracks. */
 
 /* 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 "bed.h"
 #include "options.h"
 
 char *browserName = NULL; /* Name of browser for example: hgwdev-sugnet.cse */
 void usage()
 {
 errAbort("bedToFrames - Makes html files for browsing custom bed track\n"
 	 "using frames. Use -pad for padding\n"
 	 "usage:\n"
 	 "   bedToFrames db bedFileIn.bed htmlTableFile.html htmlFrameFile.html url\n"
 	 "-browserName=browserName (i.e. genome-test.cse)"
 	 );
 }
 
 void writeOutFrames(FILE *htmlFrame, char *fileName, char *db, char *url, struct bed *bed)
 /** Write out frame for htmls. */
 {
 fprintf(htmlFrame, "<html><head><title>Bed Custom Track</title></head>\n"
 	"<frameset cols=\"18%%,82%%\">\n"
 	"<frame name=\"_list\" src=\"./%s\">\n"
 	"<frame name=\"browser\" src=\"http://%s.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s:%d-%d&"
 	"hgt.customText=%s\">\n"
 	"</frameset>\n"
 	"</html>\n", fileName, browserName, db, bed->chrom, bed->chromStart, bed->chromEnd, url) ;
 }
 
 void bedToFrames(char *db, char *bedFile, char *html, char *frame, char *url)
 /* Load the beds and print the custom file. */
 {
 struct bed *bedList=NULL, *bed = NULL;
 FILE *htmlFrame = NULL, *htmlOut=NULL;
 int padding = optionInt("pad", 100);
 boolean score = optionExists("score");
 warn("Padding is: %d", padding);
 browserName = optionVal("browserName", "genome");
 bedList = bedLoadAll(bedFile);
 if(score) 
     {
     slSort(&bedList, bedCmpScore);
     slReverse(&bedList);
     }
 else
     {
     slSort(&bedList, bedCmp);
     }
 htmlFrame = mustOpen(frame, "w");
 
 writeOutFrames(htmlFrame, html, db, url, bedList);
 carefulClose(&htmlFrame);
 
 htmlOut = mustOpen(html, "w");
 fprintf(htmlOut, "<html><body><ol>\n");
 for(bed=bedList; bed != NULL; bed = bed->next)
     {
     fprintf(htmlOut, "<li><a target=\"browser\" "
 	    "href=\"http://%s.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s:%d-%d\"> "
 	    "%s %d</a></li>\n", 
 	    browserName,db, bed->chrom, bed->chromStart-padding, bed->chromEnd+padding, bed->name, score ? bed->score : 0);
     }
 fprintf(htmlOut, "</body></html>\n");
 carefulClose(&htmlOut);
 bedFreeList(&bedList);
 }
 
 int main(int argc, char *argv[])
 {
 optionHash(&argc, argv);
 if(argc != 6)
     usage();
 bedToFrames(argv[1], argv[2], argv[3], argv[4], argv[5]);
 return 0;
 }