/**
* Constructs an object which will redirect into a different file.
*
* <p>Note that this function does not respect the isCompressed() request from the stub, in order
* to ensure that tmp. files can be read back in by the Tribble system, and merged with the
* mergeInto function.
*
* @param stub Stub to use when synthesizing file / header info.
* @param tempFile File into which to direct the output data.
*/
public VariantContextWriterStorage(VariantContextWriterStub stub, File tempFile) {
// logger.debug("Creating temporary output file " + tempFile.getAbsolutePath() + " for
// VariantContext output.");
this.file = tempFile;
this.writer = vcfWriterToFile(stub, file, false, false);
writer.writeHeader(stub.getVCFHeader());
}
/**
* common initialization routine for multiple constructors
*
* @param stub Stub to use when constructing the output file.
* @param file Target file into which to write VCF records.
* @param indexOnTheFly true to index the file on the fly. NOTE: will be forced to false for
* compressed files.
* @param allowCompressed if false, we won't compress the output, even if the stub requests it.
* Critical for creating temp. output files that will be subsequently merged, as these do not
* support compressed output
* @return A VCF writer for use with this class
*/
private VariantContextWriter vcfWriterToFile(
final VariantContextWriterStub stub,
final File file,
final boolean indexOnTheFly,
final boolean allowCompressed) {
try {
// we cannot merge compressed outputs, so don't compress if allowCompressed is false,
// which is the case when we have a temporary output file for later merging
if (allowCompressed && stub.isCompressed()) stream = new BlockCompressedOutputStream(file);
else
stream = new PrintStream(new BufferedOutputStream(new FileOutputStream(file), BUFFER_SIZE));
} catch (IOException ex) {
throw new UserException.CouldNotCreateOutputFile(
file, "Unable to open target output stream", ex);
}
// The GATK/Tribble can't currently index block-compressed files on the fly. Disable OTF
// indexing even if the user explicitly asked for it.
EnumSet<Options> options = stub.getWriterOptions(indexOnTheFly);
VariantContextWriter writer =
VariantContextWriterFactory.create(
file, this.stream, stub.getMasterSequenceDictionary(), options);
// if the stub says to test BCF, create a secondary writer to BCF and an 2 way out writer to
// send to both
// TODO -- remove me when argument generateShadowBCF is removed
if (stub.alsoWriteBCFForTest() && !VariantContextWriterFactory.isBCFOutput(file, options)) {
final File bcfFile = BCF2Utils.shadowBCF(file);
if (bcfFile != null) {
VariantContextWriter bcfWriter =
VariantContextWriterFactory.create(
bcfFile, stub.getMasterSequenceDictionary(), options);
writer = new TestWriter(writer, bcfWriter);
}
}
return writer;
}
/**
* Constructs an object which will write directly into the output file provided by the stub.
* Intentionally delaying the writing of the header -- this should be filled in by the walker.
*
* <p>Respecs the isCompressed() request in stub, so if isCompressed() is true then this will
* create a storage output that dumps output to a BlockCompressedOutputStream.
*
* @param stub Stub to use when constructing the output file.
*/
public VariantContextWriterStorage(VariantContextWriterStub stub) {
if (stub.getOutputFile() != null) {
this.file = stub.getOutputFile();
writer = vcfWriterToFile(stub, stub.getOutputFile(), true, true);
} else if (stub.getOutputStream() != null) {
this.file = null;
this.stream = stub.getOutputStream();
writer =
VariantContextWriterFactory.create(
stream, stub.getMasterSequenceDictionary(), stub.getWriterOptions(false));
} else
throw new ReviewedStingException(
"Unable to create target to which to write; storage was provided with neither a file nor a stream.");
}