/**
* 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();
}
public void toTDF(
String typeString,
String ifile,
String ofile,
String probeFile,
String genomeId,
int maxZoomValue,
Collection<WindowFunction> windowFunctions,
String tmpDirName,
int maxRecords)
throws IOException, PreprocessingException {
if (!ifile.endsWith(".affective.csv")) validateIsTilable(typeString);
System.out.println("toTDF. File = " + ifile);
System.out.println("Max zoom = " + maxZoomValue);
if (probeFile != null && probeFile.trim().length() > 0) {
System.out.println("Probe file = " + probeFile);
}
System.out.print("Window functions: ");
for (WindowFunction wf : windowFunctions) {
System.out.print(wf.toString() + " ");
}
System.out.println();
boolean isGCT = isGCT(typeString);
Genome genome = loadGenome(genomeId, isGCT);
if (genome == null) {
throw new PreprocessingException("Genome could not be loaded: " + genomeId);
}
File inputFileOrDir = new File(ifile);
// Estimae the total number of lines to be parsed, for progress updates
int nLines = estimateLineCount(inputFileOrDir);
// TODO -- move this block of code out of here, this should be done before calling this method
// Convert gct files to igv format first
File deleteme = null;
if (isGCT(typeString)) {
File tmpDir = null;
if (tmpDirName != null && tmpDirName.length() > 0) {
tmpDir = new File(tmpDirName);
if (!tmpDir.exists() || !tmpDir.isDirectory()) {
throw new PreprocessingException(
"Specified tmp directory does not exist or is not directory: " + tmpDirName);
}
} else {
tmpDir = new File(System.getProperty("java.io.tmpdir"), System.getProperty("user.name"));
}
if (!tmpDir.exists()) {
tmpDir.mkdir();
}
String baseName = (new File(ifile)).getName();
File igvFile = new File(tmpDir, baseName + ".igv");
igvFile.deleteOnExit();
doGCTtoIGV(typeString, ifile, igvFile, probeFile, maxRecords, tmpDirName, genome);
inputFileOrDir = igvFile;
deleteme = igvFile;
typeString = ".igv";
}
// Convert to tdf
File outputFile = new File(ofile);
try {
Preprocessor p = new Preprocessor(outputFile, genome, windowFunctions, nLines, null);
if (inputFileOrDir.isDirectory() || inputFileOrDir.getName().endsWith(".list")) {
List<File> files = getFilesFromDirOrList(inputFileOrDir);
for (File f : files) {
p.preprocess(f, maxZoomValue, typeString);
}
} else {
p.preprocess(inputFileOrDir, maxZoomValue, typeString);
}
p.finish();
} catch (IOException e) {
e.printStackTrace();
// Delete output file as its probably corrupt
if (outputFile.exists()) {
outputFile.delete();
}
} finally {
if (deleteme != null && deleteme.exists()) {
deleteme.delete();
}
}
System.out.flush();
}