/* (non-Javadoc)
* @see edu.usc.epigenome.genomeLibs.MethylDb.CpgWalker.CpgWalker#processWindow(java.util.List)
*/
@Override
protected void processWindow(List<Cpg> inWindow) {
checkWriter();
super.processWindow(inWindow);
int windMidpoint =
(int)
Math.round(
((double) (CpgWalker.windEnd(inWindow) + CpgWalker.windStart(inWindow))) / 2.0);
double meth = this.methSummarizer.get(0).getValMean(true);
int winds = CpgWalker.windStart(inWindow);
int winde = CpgWalker.windEnd(inWindow);
// System.err.printf("Processing window CpgWalkerWigWriter: %s\tmeth=%.2f\n",
// CpgWalker.windStr(inWindow), meth);
// First wig writer
wigWriter.printf("%d\t%d\n", windMidpoint, (int) Math.round(100.0 * meth));
// Then bedgraph
if (bedgraphWriter != null) {
int midpointMidpoint =
(int) Math.floor(((double) lastWindMidpoint + (double) windMidpoint) / 2.0);
int spanStart = lastSpanEnd + 1;
int spanEnd =
(this.lastWindMidpoint > 0) ? midpointMidpoint : -1; // This isn't really correct
// Don't do it if we're on the first one of the chromosome.
if (this.lastSpanEnd > 0) {
if (this.csvMode) {
bedgraphWriter.printf(
"%d,%d,%d,%d,%d\n",
this.curChrNum, winds, winde, (int) Math.round(100.0 * lastMeth), inWindow.size());
} else {
bedgraphWriter.printf(
"%s\t%d\t%d\t%d\n",
this.curChr, spanStart, spanEnd, (int) Math.round(100.0 * lastMeth));
}
}
// System.err.printf("\t%s\t%d\t%d\t%d\t%d\n",this.curChr, winds, winde,
// (int)Math.round(100.0*lastMeth), winde-winds);
this.lastSpanEnd = spanEnd;
this.lastWindMidpoint = windMidpoint;
this.lastMeth = meth;
}
}
/* (non-Javadoc)
* @see edu.usc.epigenome.genomeLibs.MethylDb.CpgWalker.CpgWalker#init()
*/
@Override
protected void init() {
super.init();
try {
System.err.printf("Initializing CpgWalkerWigWriter: %s\n", this.walkParams.toString());
} catch (Exception e) {
}
}
/* (non-Javadoc)
* @see edu.usc.epigenome.genomeLibs.MethylDb.CpgWalker.CpgWalker#alertNewChrom()
*/
@Override
protected void alertNewChrom() {
super.alertNewChrom();
this.curChrNum = (new ChromFeatures()).chrom_from_public_str(this.curChr);
System.err.printf("New chrom: %s\n", this.curChr);
checkWriter();
wigWriter.printf("variableStep chrom=%s\n", this.curChr);
lastWindMidpoint = -1;
lastSpanEnd = -1;
lastMeth = -1.0;
}
/* (non-Javadoc)
* @see edu.usc.epigenome.genomeLibs.MethylDb.CpgWalker.CpgWalker#finishChr()
*/
@Override
public void finishChr() {
super.finishChr();
checkWriter();
}