public String[] getSamples() {
if (this.tribbleFeatureSource.isIndexed()) {
// Load the index for meta information. Its already loaded, but not public in the htsjdk
// class.
Index idx = loadIndex(this.locator.getPath());
if (idx != null) {
Map<String, String> map = idx.getProperties();
if (map != null && map.containsKey("samples")) {
return Globals.commaPattern.split(map.get("samples"));
}
}
}
// Try to fetch features from codec. This is to support a deprecated option to
// specify sample names in the .mut or .maf file header.
MUTCodec codec = new MUTCodec(locator.getPath(), null);
return codec.getSamples();
}
public static Sorter getSorter(File inputFile, File outputFile) {
String shortFN = inputFile.getName().toLowerCase();
if (shortFN.endsWith(".txt")) {
shortFN = shortFN.substring(0, shortFN.length() - 4);
}
if (shortFN.endsWith(".cn")
|| shortFN.endsWith(".xcn")
|| shortFN.endsWith(".snp")
|| shortFN.endsWith(".igv")) {
return new CNSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".sam")) {
return new SAMSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".aligned")
|| shortFN.endsWith(".bed")
|| shortFN.endsWith(".bedgraph")
|| shortFN.endsWith(".bdg")) {
return new BedSorter(inputFile, outputFile);
} else if (GFFFeatureSource.isGFF(shortFN)) {
return new GFFSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".vcf")) {
return new VCFSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".psl") || shortFN.endsWith(".pslx")) {
return new BedSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".eqtl")) {
return new EQTLSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".snp")) {
return new GenericSorter(inputFile, outputFile, 1, 2);
} else if (GWASParser.isGWASFile(shortFN)) {
return new GWASSorter(inputFile, outputFile);
} else if (MUTCodec.isMutationAnnotationFile(
new ResourceLocator(inputFile.getAbsolutePath()))) {
return new MUTSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".interaction")) {
return new InteractionSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".bam")) {
return new BAMSorter(inputFile, outputFile);
} else {
log.error("Unknown file type or sorting not supported for: " + inputFile.getName());
return null;
}
}