/**
* Compute coverage or density of an alignment or feature file.
*
* @param ifile Alignment or feature file
* @param ofile Output file
* @param genomeId Genome id (e.g. hg18) or full path to a .genome file (e.g.
* /xchip/igv/scer2.genome)
* @param maxZoomValue Maximum zoom level to precompute. Default value is 7
* @param windowFunctions
* @param windowSizeValue
* @param extFactorValue
* @param trackLine
* @param queryString
* @param minMapQuality
* @param countFlags
* @throws IOException
*/
public void doCount(
String ifile,
String ofile,
String genomeId,
int maxZoomValue,
Collection<WindowFunction> windowFunctions,
int windowSizeValue,
int extFactorValue,
String trackLine,
String queryString,
int minMapQuality,
int countFlags)
throws IOException {
System.out.println("Computing coverage. File = " + ifile);
System.out.println("Max zoom = " + maxZoomValue);
System.out.println("Window size = " + windowSizeValue);
System.out.print("Window functions: ");
for (WindowFunction wf : windowFunctions) {
System.out.print(wf.toString() + " ");
}
System.out.println();
System.out.println("Ext factor = " + extFactorValue);
Genome genome = loadGenome(genomeId, false);
if (genome == null) {
throw new PreprocessingException("Genome could not be loaded: " + genomeId);
}
// Multiple files allowed for count command (a tdf and a wig)
File tdfFile = null;
File wigFile = null;
String[] files = ofile.split(",");
if (files[0].endsWith("wig")) {
wigFile = new File(files[0]);
} else {
tdfFile = new File(files[0]);
}
if (files.length > 1) {
if (files[1].endsWith("wig")) {
wigFile = new File(files[1]);
} else if (files[1].endsWith("tdf")) {
tdfFile = new File(files[1]);
}
}
if (tdfFile != null && !tdfFile.getName().endsWith(".tdf")) {
tdfFile = new File(tdfFile.getAbsolutePath() + ".tdf");
}
Preprocessor p = new Preprocessor(tdfFile, genome, windowFunctions, -1, null);
// p.count(ifile, windowSizeValue, extFactorValue, maxZoomValue, wigFile, coverageOpt,
// trackLine);
p.count(
ifile,
windowSizeValue,
extFactorValue,
maxZoomValue,
wigFile,
trackLine,
queryString,
minMapQuality,
countFlags);
p.finish();
System.out.flush();
}
