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/*
* The MIT License (MIT)
* Copyright (c) 2016-2017 Intel Corporation
* Copyright (c) 2018-2019 Omics Data Automation, Inc.
*
* 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 org.genomicsdb.reader;
import org.genomicsdb.GenomicsDBLibLoader;
import org.genomicsdb.exception.GenomicsDBException;
import org.genomicsdb.model.GenomicsDBExportConfiguration;
import java.io.IOException;
import java.io.InputStream;
/**
* Provides a java.io.InputStream interface for the GenomicsDB combine gVCF operation.
* It can be used as to construct a
*
* PositionalBufferedStream object.The PositionalBufferedStream object can
* then be used by FeatureCodecs such as BCF2Codec to construct VariantContext objects
*/
public class GenomicsDBQueryStream extends InputStream {
private static final boolean DEFAULT_READ_AS_BCF = true;
private static final boolean DEFAULT_USE_MISSING_ONLY_NOT_VECTOR_END = true;
private static final boolean DEFAULT_KEEP_IDX_FIELDS_IN_HEADER = false;
static {
try {
boolean loaded = GenomicsDBLibLoader.loadLibrary();
if(!loaded) throw new GenomicsDBException("Could not load genomicsdb native library");
} catch(UnsatisfiedLinkError ule) {
throw new GenomicsDBException("Could not load genomicsdb native library", ule);
}
}
//"Pointer" to TileDB/GenomicsDB read state object
private long readStateHandle = 0;
/**
* Constructor
* @param loaderJSONFile GenomicsDB loader JSON configuration file
* @param queryPB GenomicsDB query protobuf
* @throws IOException when data cannot be read from the stream
*/
public GenomicsDBQueryStream(final String loaderJSONFile,
final GenomicsDBExportConfiguration.ExportConfiguration queryPB) throws IOException {
this(loaderJSONFile, queryPB, "", 0, 0);
}
/**
* Constructor
* @param loaderJSONFile GenomicsDB loader JSON configuration file
* @param queryPB GenomicsDB query protobuf
* @param readAsBCF serialize-deserialize VCF records as BCF2 records
* @throws IOException when data cannot be read from the stream
*/
public GenomicsDBQueryStream(final String loaderJSONFile,
final GenomicsDBExportConfiguration.ExportConfiguration queryPB, final boolean readAsBCF) throws IOException {
this(loaderJSONFile, queryPB, readAsBCF, false);
}
/**
* Constructor
* @param loaderJSONFile GenomicsDB loader JSON configuration file
* @param queryPB GenomicsDB query protobuf
* @param readAsBCF serialize-deserialize VCF records as BCF2 records
* @param produceHeaderOnly produce only the header
* @throws IOException when data cannot be read from the stream
*/
public GenomicsDBQueryStream(final String loaderJSONFile,
final GenomicsDBExportConfiguration.ExportConfiguration queryPB, final boolean readAsBCF,
final boolean produceHeaderOnly) throws IOException {
this(loaderJSONFile, queryPB, "", 0, 0, 0, 10485760,10485760,
readAsBCF, produceHeaderOnly);
}
/**
* Constructor
* @param loaderJSONFile GenomicsDB loader JSON configuration file
* @param queryPB GenomicsDB query protobuf
* @param chr contig name
* @param start start position (1-based)
* @param end end position, inclusive (1-based)
* @throws IOException when data cannot be read from the stream
*/
public GenomicsDBQueryStream(final String loaderJSONFile,
final GenomicsDBExportConfiguration.ExportConfiguration queryPB, final String chr,
final long start, final long end) throws IOException {
this(loaderJSONFile, queryPB, chr, start, end, 0);
}
/**
* Constructor
* @param loaderJSONFile GenomicsDB loader JSON configuration file
* @param queryPB GenomicsDB query protobuf
* @param chr contig name
* @param start start position (1-based)
* @param end end position, inclusive (1-based)
* @param readAsBCF serialize-deserialize VCF records as BCF2 records
* @throws IOException when data cannot be read from the stream
*/
public GenomicsDBQueryStream(final String loaderJSONFile,
final GenomicsDBExportConfiguration.ExportConfiguration queryPB, final String chr,
final long start, final long end, final boolean readAsBCF) throws IOException {
this(loaderJSONFile, queryPB, chr, start, end, 0, 10485760, 10485760,
readAsBCF, false);
}
/**
* Constructor
* @param loaderJSONFile GenomicsDB loader JSON configuration file
* @param queryPB GenomicsDB query protobuf
* @param chr contig name
* @param start start position (1-based)
* @param end end position, inclusive (1-based)
* @param rank rank of this object if launched from within an MPI context (not used)
* @throws IOException when data cannot be read from the stream
*/
public GenomicsDBQueryStream(final String loaderJSONFile,
final GenomicsDBExportConfiguration.ExportConfiguration queryPB, final String chr,
final long start, final long end, final int rank) throws IOException {
this(loaderJSONFile, queryPB, chr, start, end, rank, 10485760, 10485760);
}
/**
* Constructor
* @param loaderJSONFile GenomicsDB loader JSON configuration file
* @param queryPB GenomicsDB query protobuf
* @param chr contig name
* @param start start position (1-based)
* @param end end position, inclusive (1-based)
* @param rank rank of this object if launched from within an MPI context (not used)
* @param bufferCapacity size of buffer in bytes to be used by the native layer
* to store combined BCF2 records
* @param segmentSize buffer to be used for querying TileDB
* @throws IOException when data cannot be read from the stream
*/
public GenomicsDBQueryStream(final String loaderJSONFile,
final GenomicsDBExportConfiguration.ExportConfiguration queryPB, final String chr,
final long start, final long end, final int rank, final long bufferCapacity,
final long segmentSize) throws IOException {
this(loaderJSONFile, queryPB, chr, start, end, rank, bufferCapacity, segmentSize, DEFAULT_READ_AS_BCF, false);
}
/**
* Constructor
* @param loaderJSONFile GenomicsDB loader JSON configuration file
* @param queryPB GenomicsDB query protobuf
* @param chr contig name
* @param start start position (1-based)
* @param end end position, inclusive (1-based)
* @param rank rank of this object if launched from within an MPI context (not used)
* @param bufferCapacity size of buffer in bytes to be used by the native layer
* to store combined BCF2 records
* @param segmentSize buffer to be used for querying TileDB
* @param readAsBCF serialize-deserialize VCF records as BCF2 records
* @param produceHeaderOnly produce VCF/BCF header only - no records (minor optimization)
* @throws IOException when data cannot be read from the stream
*/
public GenomicsDBQueryStream(final String loaderJSONFile,
final GenomicsDBExportConfiguration.ExportConfiguration queryPB, final String chr,
final long start, final long end, final int rank, final long bufferCapacity,
final long segmentSize, final boolean readAsBCF, final boolean produceHeaderOnly) throws IOException {
this(loaderJSONFile, queryPB, chr, start, end, rank, bufferCapacity, segmentSize, readAsBCF,
produceHeaderOnly, DEFAULT_USE_MISSING_ONLY_NOT_VECTOR_END, DEFAULT_KEEP_IDX_FIELDS_IN_HEADER);
}
/**
* Constructor
* @param loaderJSONFile GenomicsDB loader JSON configuration file
* @param queryPB GenomicsDB query protobuf
* @param chr contig name
* @param start start position (1-based)
* @param end end position, inclusive (1-based)
* @param rank rank of this object if launched from within an MPI context (not used)
* @param bufferCapacity size of buffer in bytes to be used by the native layer
* to store combined BCF2 records
* @param segmentSize buffer to be used for querying TileDB
* @param readAsBCF serialize-deserialize VCF records as BCF2 records
* @param produceHeaderOnly produce VCF/BCF header only - no records (minor optimization)
* @param useMissingValuesOnlyNotVectorEnd don't add BCF2.2 vector end values
* @param keepIDXFieldsInHeader keep BCF IDX fields in header
* @throws IOException when data cannot be read from the stream
*/
public GenomicsDBQueryStream(final String loaderJSONFile,
final GenomicsDBExportConfiguration.ExportConfiguration queryPB, final String chr,
final long start, final long end, final int rank, final long bufferCapacity,
final long segmentSize, final boolean readAsBCF, final boolean produceHeaderOnly,
final boolean useMissingValuesOnlyNotVectorEnd, final boolean keepIDXFieldsInHeader) throws IOException {
if (queryPB.isInitialized()) {
readStateHandle = jniGenomicsDBInit(loaderJSONFile, queryPB.toByteArray(), chr, start, end, rank,
bufferCapacity, segmentSize, readAsBCF, produceHeaderOnly, useMissingValuesOnlyNotVectorEnd,
keepIDXFieldsInHeader);
if (readStateHandle == 0L) {
throw new IOException("GenomicsDBQueryStream jniGenomicsDBInit error");
}
} else {
throw new IOException("GenomicsDBQueryStream export configuration input argument is not initialized and/or validated");
}
}
/*
* Returns a "pointer" to a structure that stores the TileDB/GenomicsDB read state
* This might look scary, but follows the same idea used in Java's compression library
*/
private native long jniGenomicsDBInit(String loaderJSONFile, byte[] queryConfigPBBuffer, String chr, long start, long end,
int rank, long bufferCapacity, long segmentSize, boolean readAsBCF,
boolean produceHeaderOnly, boolean useMissingValuesOnlyNotVectorEnd,
boolean keepIDXFieldsInHeader) throws IOException;
private native long jniGenomicsDBClose(long handle);
private native long jniGenomicsDBGetNumBytesAvailable(long handle);
private native byte jniGenomicsDBReadNextByte(long handle);
private native int jniGenomicsDBRead(long handle, byte[] buffer, int off, int len);
private native long jniGenomicsDBSkip(long handle, long n);
@Override
public int available() throws IOException {
return (int)jniGenomicsDBGetNumBytesAvailable(readStateHandle);
}
@Override
public void close() throws IOException {
readStateHandle = jniGenomicsDBClose(readStateHandle);
}
@Override
public boolean markSupported()
{
return false;
}
@Override
public int read() throws IOException {
return jniGenomicsDBReadNextByte(readStateHandle);
}
@Override
public int read(byte[] buffer, int off, int len) throws IOException {
if (len <= 0) return 0;
long numBytesRead = jniGenomicsDBRead(readStateHandle, buffer, off, len);
return (numBytesRead == 0) ? -1 : (int)numBytesRead;
}
@Override
public long skip(long n) throws IOException {
return jniGenomicsDBSkip(readStateHandle, n);
}
}
