/**
* @see org.broad.tribble.index.linear.LinearIndex#optimize(double)
* @param featureInput File containing features
* @param codec Codec used to read the features
* @param optimizeThreshold Threshold used to optimize the linear index
* @return
*/
public static long runWithIndex(File featureInput, FeatureCodec codec, int optimizeThreshold) {
// get an index
Index index = loadIndex(featureInput, codec);
if (optimizeThreshold != -1) ((LinearIndex) index).optimize(optimizeThreshold);
// get a reader
AbstractFeatureReader reader = null;
try {
reader = AbstractFeatureReader.getFeatureReader(featureInput.getAbsolutePath(), codec, index);
// now read iterate over the file
long recordCount = 0l;
// this call could be replaced with a query
Iterator<Feature> iter = reader.iterator();
// cycle through the iterators
while (iter.hasNext()) {
Feature feat = iter.next();
++recordCount;
}
System.err.println("We saw " + recordCount + " record in file " + featureInput);
return recordCount;
} catch (IOException e) {
throw new RuntimeException(
"Something went wrong while reading feature file " + featureInput, e);
}
}
public void mergeInto(VariantContextWriterStorage target) {
try {
if (!closed)
throw new ReviewedStingException("Writer not closed, but we are merging into the file!");
final String targetFilePath =
target.file != null ? target.file.getAbsolutePath() : "/dev/stdin";
logger.debug(
String.format(
"Merging VariantContextWriterStorage from %s into %s",
file.getAbsolutePath(), targetFilePath));
// use the feature manager to determine the right codec for the tmp file
// that way we don't assume it's a specific type
final FeatureManager.FeatureDescriptor fd = new FeatureManager().getByFiletype(file);
if (fd == null) throw new UserException.LocalParallelizationProblem(file);
final FeatureCodec codec = fd.getCodec();
final AbstractFeatureReader<Feature, ?> source =
AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), codec, false);
for (final Feature vc : source.iterator()) {
target.writer.add((VariantContext) vc);
}
source.close();
file.delete(); // this should be last to aid in debugging when the process fails
} catch (IOException e) {
throw new UserException.CouldNotReadInputFile(
file, "Error reading file in VCFWriterStorage: ", e);
}
}
