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/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package htsjdk.variant.variantcontext.writer;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.LocationAware;
import htsjdk.samtools.util.RuntimeIOException;
import htsjdk.tribble.index.DynamicIndexCreator;
import htsjdk.tribble.index.Index;
import htsjdk.tribble.index.IndexCreator;
import htsjdk.tribble.index.IndexFactory;
import htsjdk.samtools.util.PositionalOutputStream;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFHeader;
import java.io.File;
import java.io.IOException;
import java.io.OutputStream;
import java.io.PrintStream;
import java.nio.file.Path;
/**
* this class writes VCF files
*/
abstract class IndexingVariantContextWriter implements VariantContextWriter {
private final String name;
private final Path location;
private final SAMSequenceDictionary refDict;
private OutputStream outputStream;
private LocationAware locationSource = null;
private IndexCreator indexer = null;
private IndexingVariantContextWriter(final String name, final Path location, final OutputStream output, final SAMSequenceDictionary refDict) {
this.name = name;
this.location = location;
this.outputStream = output;
this.refDict = refDict;
}
static String DEFAULT_READER_NAME = "Reader Name";
/**
* Create a VariantContextWriter with an associated index using the default index creator
*
* @param name the name of this writer (i.e. the file name or stream)
* @param location the path to the output file
* @param output the output stream to write to
* @param refDict the reference dictionary
* @param enableOnTheFlyIndexing is OTF indexing enabled?
*/
protected IndexingVariantContextWriter(final String name, final File location, final OutputStream output, final SAMSequenceDictionary refDict,
final boolean enableOnTheFlyIndexing) {
this(name, IOUtil.toPath(location), output, refDict, enableOnTheFlyIndexing);
}
/**
* Create a VariantContextWriter with an associated index using the default index creator
*
* @param name the name of this writer (i.e. the file name or stream)
* @param location the path to the output file
* @param output the output stream to write to
* @param refDict the reference dictionary
* @param enableOnTheFlyIndexing is OTF indexing enabled?
*/
protected IndexingVariantContextWriter(final String name, final Path location, final OutputStream output, final SAMSequenceDictionary refDict,
final boolean enableOnTheFlyIndexing) {
this(name, location, output, refDict);
if ( enableOnTheFlyIndexing ) {
initIndexingWriter(new DynamicIndexCreator(location, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME));
}
}
/**
* Create a VariantContextWriter with an associated index using a custom index creator
*
* @param name the name of this writer (i.e. the file name or stream)
* @param location the path to the output file
* @param output the output stream to write to
* @param refDict the reference dictionary
* @param enableOnTheFlyIndexing is OTF indexing enabled?
* @param idxCreator the custom index creator. NOTE: must be initialized
*/
protected IndexingVariantContextWriter(final String name, final File location, final OutputStream output, final SAMSequenceDictionary refDict,
final boolean enableOnTheFlyIndexing, final IndexCreator idxCreator) {
this(name, IOUtil.toPath(location), output, refDict, enableOnTheFlyIndexing, idxCreator);
}
/**
* Create a VariantContextWriter with an associated index using a custom index creator
*
* @param name the name of this writer (i.e. the file name or stream)
* @param location the path to the output file
* @param output the output stream to write to
* @param refDict the reference dictionary
* @param enableOnTheFlyIndexing is OTF indexing enabled?
* @param idxCreator the custom index creator. NOTE: must be initialized
*/
protected IndexingVariantContextWriter(final String name, final Path location, final OutputStream output, final SAMSequenceDictionary refDict,
final boolean enableOnTheFlyIndexing, final IndexCreator idxCreator) {
this(name, location, output, refDict);
if ( enableOnTheFlyIndexing ) {
// TODO: Handle non-Tribble IndexCreators
initIndexingWriter(idxCreator);
}
}
private void initIndexingWriter(final IndexCreator idxCreator) {
indexer = idxCreator;
if (outputStream instanceof LocationAware) {
locationSource = (LocationAware)outputStream;
} else {
final PositionalOutputStream positionalOutputStream = new PositionalOutputStream(outputStream);
locationSource = positionalOutputStream;
outputStream = positionalOutputStream;
}
}
/** return true is the underlying stream is a PrintStream and
* its checkError returned true. Used to stop linux pipelines
*/
@Override
public boolean checkError() {
return (getOutputStream() instanceof PrintStream) &&
PrintStream.class.cast(getOutputStream()).checkError();
}
public OutputStream getOutputStream() {
return outputStream;
}
public String getStreamName() {
return name;
}
@Override
public abstract void writeHeader(VCFHeader header);
/**
* attempt to close the VCF file
*/
@Override
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) {
indexer.setIndexSequenceDictionary(refDict);
final Index index = indexer.finalizeIndex(locationSource.getPosition());
index.writeBasedOnFeaturePath(location);
}
} catch (final IOException e) {
throw new RuntimeIOException("Unable to close index for " + getStreamName(), e);
}
}
/**
* @return the reference sequence dictionary used for the variant contexts being written
*/
public SAMSequenceDictionary getRefDict() {
return refDict;
}
/**
* add a record to the file
*
* @param vc the Variant Context object
*/
@Override
public void add(final VariantContext vc) {
// if we are doing on the fly indexing, add the record ***before*** we write any bytes
if ( indexer != null )
indexer.addFeature(vc, locationSource.getPosition());
}
/**
* Returns a reasonable "name" for this writer, to display to the user if something goes wrong
*
* @param location
* @param stream
* @return
*/
protected static final String writerName(final File location, final OutputStream stream) {
return writerName(IOUtil.toPath(location), stream);
}
/**
* Returns a reasonable "name" for this writer, to display to the user if something goes wrong
*
* @param location
* @param stream
* @return
*/
protected static final String writerName(final Path location, final OutputStream stream) {
return location == null ? stream == null ? DEFAULT_READER_NAME : stream.toString() : location.toAbsolutePath().toUri().toString();
}
}
