/* 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 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, "Bed Custom Track\n"
"\n"
"\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, "\n");
for(bed=bedList; bed != NULL; bed = bed->next)
{
fprintf(htmlOut, "- "
"%s %d
\n",
browserName,db, bed->chrom, bed->chromStart-padding, bed->chromEnd+padding, bed->name, score ? bed->score : 0);
}
fprintf(htmlOut, "\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;
}