/**
* creates a new index, given the feature file and the codec
*
* @param featureFile the feature file (i.e. .vcf, .bed)
* @param indexFile the index file; the location we should be writing the index to
* @param codec the codec to read features with
* @return an index instance
*/
public static Index createAndWriteNewIndex(File featureFile, File indexFile, FeatureCodec codec) {
try {
Index index = IndexFactory.createLinearIndex(featureFile, codec);
// try to write it to disk
LittleEndianOutputStream stream =
new LittleEndianOutputStream(new FileOutputStream(indexFile));
index.write(stream);
stream.close();
return index;
} catch (IOException e) {
throw new RuntimeException("Unable to create index from file " + featureFile, e);
}
}
/** attempt to close the VCF file */
public void close() {
try {
// close the underlying output stream
outputStream.close();
// close the index stream (keep it separate to help debugging efforts)
if (indexer != null) {
final Index index = indexer.finalizeIndex(positionalOutputStream.getPosition());
setIndexSequenceDictionary(index, refDict);
index.write(idxStream);
idxStream.close();
}
} catch (IOException e) {
throw new RuntimeException("Unable to close index for " + getStreamName(), e);
}
}
private static void setIndexSequenceDictionary(
final Index index, final SAMSequenceDictionary dict) {
for (final SAMSequenceRecord seq : dict.getSequences()) {
final String contig = SequenceDictionaryPropertyPredicate + seq.getSequenceName();
final String length = String.valueOf(seq.getSequenceLength());
index.addProperty(contig, length);
}
}
/** attempt to close the VCF file */
public void close() {
// try to close the vcf stream
try {
mWriter.flush();
mWriter.close();
} catch (IOException e) {
throw new TribbleException(
"Unable to close " + locationString() + " because of " + e.getMessage());
}
// try to close the index stream (keep it separate to help debugging efforts)
if (indexer != null) {
try {
Index index = indexer.finalizeIndex(positionalStream.getPosition());
index.write(idxStream);
idxStream.close();
} catch (IOException e) {
throw new TribbleException(
"Unable to close index for " + locationString() + " because of " + e.getMessage());
}
}
}
/**
* Create a tribble style index.
*
* @param ifile
* @param outputFile
* @param indexType
* @param binSize
* @throws IOException
*/
private void createTribbleIndex(
String ifile, File outputFile, int indexType, int binSize, FeatureCodec codec)
throws IOException {
File inputFile = new File(ifile);
Index idx = null;
if (indexType == LINEAR_INDEX) {
idx = IndexFactory.createLinearIndex(inputFile, codec, binSize);
} else {
idx = IndexFactory.createIntervalIndex(inputFile, codec, binSize);
}
if (idx != null) {
String idxFile;
if (outputFile != null) {
idxFile = outputFile.getAbsolutePath();
} else {
idxFile = ifile + ".idx";
}
LittleEndianOutputStream stream = null;
try {
stream =
new LittleEndianOutputStream(new BufferedOutputStream(new FileOutputStream(idxFile)));
idx.write(stream);
} catch (Exception e) {
e.printStackTrace();
// Delete output file as its probably corrupt
File tmp = new File(idxFile);
if (tmp.exists()) {
tmp.delete();
}
} finally {
if (stream != null) {
stream.close();
}
}
}
}
