/* (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;
}
}
