@Override
protected Index doInBackground() throws Exception {
int binSize = IgvTools.LINEAR_BIN_SIZE;
FeatureCodec codec =
CodecFactory.getCodec(
file.getAbsolutePath(), GenomeManager.getInstance().getCurrentGenome());
if (codec != null) {
try {
Index index = IndexFactory.createLinearIndex(file, codec, binSize);
if (index != null) {
IgvTools.writeTribbleIndex(index, idxFile.getAbsolutePath());
}
return index;
} catch (TribbleException.MalformedFeatureFile e) {
StringBuffer buf = new StringBuffer();
buf.append("<html>Files must be sorted by start position prior to indexing.<br>");
buf.append(e.getMessage());
buf.append(
"<br><br>Note: igvtools can be used to sort the file, select \"File > Run igvtools...\".");
MessageUtils.showMessage(buf.toString());
}
} else {
throw new DataLoadException("Unknown File Type", file.getAbsolutePath());
}
return null;
}
/**
* Return an parser instance appropriate the the file type. Currently the filename is used to
* determine file type, this is fragile obviously but what is the alternative?
*/
public static FeatureParser getInstanceFor(ResourceLocator locator, Genome genome) {
FeatureCodec codec = CodecFactory.getCodec(locator, genome);
if (codec != null && codec instanceof AsciiFeatureCodec) {
return new FeatureCodecParser((AsciiFeatureCodec) codec, genome);
} else {
return null;
}
}
private static FeatureCodec getCodec(String path, Genome genome) {
String tmp = getStrippedFilename(path);
return CodecFactory.getCodec(tmp, genome);
}
/**
* Create an index for an alignment or feature file The output index will have the same base name
* is the input file, although it may be in a different directory. An appropriate index extension
* (.sai, .idx, etc.) will be appended.
*
* @param ifile
* @param typeString
* @param outputDir
* @param indexType
* @param binSize
* @throws IOException
*/
public String doIndex(
String ifile, String typeString, String outputDir, int indexType, int binSize)
throws IOException {
File inputFile = new File(ifile);
if (outputDir == null) {
outputDir = inputFile.getParent();
}
String outputFileName = (new File(outputDir, inputFile.getName())).getAbsolutePath();
if (typeString.endsWith("gz")) {
System.out.println("Cannot index a gzipped file");
throw new PreprocessingException("Cannot index a gzipped file");
}
if (typeString.endsWith("bam")) {
String msg =
"Cannot index a BAM file. Use the samtools package for sorting and indexing BAM files.";
System.out.println(msg);
throw new PreprocessingException(msg);
}
// We have different naming conventions for different index files
if (typeString.endsWith("sam") && !outputFileName.endsWith(".sai")) {
outputFileName += ".sai";
} else if (typeString.endsWith("bam") && !outputFileName.endsWith(".bai")) {
outputFileName += ".bai";
} else if (typeString.endsWith("fa") && !outputFileName.endsWith(".fai")) {
outputFileName += ".fai";
} else if (typeString.endsWith("fasta") && !outputFileName.endsWith(".fai")) {
outputFileName += ".fai";
} else if (!typeString.endsWith("sam")
&& !typeString.endsWith("bam")
&& !outputFileName.endsWith(".idx")) {
outputFileName += ".idx";
}
File outputFile = new File(outputFileName);
// Sam/FASTA files are special
try {
if (typeString.endsWith("sam")) {
AlignmentIndexer indexer = AlignmentIndexer.getInstance(inputFile, null, null);
indexer.createSamIndex(outputFile);
return outputFileName;
} else if (typeString.equals(".fa") || typeString.equals(".fasta")) {
FastaUtils.createIndexFile(inputFile.getAbsolutePath(), outputFileName);
return outputFileName;
}
} catch (Exception e) {
e.printStackTrace();
// Delete output file as it is probably corrupt
if (outputFile.exists()) {
outputFile.delete();
}
}
Genome genome = null; // <= don't do chromosome conversion
FeatureCodec codec = CodecFactory.getCodec(ifile, genome);
if (codec != null) {
try {
createTribbleIndex(ifile, outputFile, indexType, binSize, codec);
} catch (TribbleException.MalformedFeatureFile e) {
StringBuffer buf = new StringBuffer();
buf.append("<html>Files must be sorted by start position prior to indexing.<br>");
buf.append(e.getMessage());
buf.append(
"<br><br>Note: igvtools can be used to sort the file, select \"File > Run igvtools...\".");
MessageUtils.showMessage(buf.toString());
}
} else {
throw new DataLoadException("Unknown File Type", ifile);
}
System.out.flush();
return outputFileName;
}
public static boolean canParse(ResourceLocator locator) {
return CodecFactory.getCodec(locator, null) != null;
}