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/*
* The MIT License
*
* Copyright (c) 2018 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.samtools;
import htsjdk.samtools.cram.io.InputStreamUtils;
import htsjdk.samtools.seekablestream.SeekablePathStream;
import htsjdk.samtools.seekablestream.SeekableStream;
import htsjdk.samtools.util.BlockCompressedInputStream;
import htsjdk.samtools.util.FileExtensions;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.RuntimeEOFException;
import java.io.IOException;
import java.io.OutputStream;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.nio.file.Files;
import java.nio.file.Path;
/**
* Writes SBI files for BAM files, as understood by {@link SBIIndex}.
*/
public final class BAMSBIIndexer {
/**
* Perform indexing on the given BAM file, at the granularity level specified.
*
* @param bamFile the path to the BAM file
* @param granularity write the offset of every n-th alignment to the index
* @throws IOException as per java IO contract
*/
public static void createIndex(final Path bamFile, final long granularity) throws IOException {
final Path splittingBaiFile = IOUtil.addExtension(bamFile, FileExtensions.SBI);
try (SeekableStream in = new SeekablePathStream(bamFile); OutputStream out = Files.newOutputStream(splittingBaiFile)) {
createIndex(in, out, granularity);
}
}
/**
* Perform indexing on the given BAM file, at the granularity level specified.
*
* @param in a seekable stream for reading the BAM file from
* @param out the stream to write the index to
* @param granularity write the offset of every n-th alignment to the index
* @throws IOException as per java IO contract
*/
public static void createIndex(final SeekableStream in, final OutputStream out, final long granularity) throws IOException {
long recordStart = SAMUtils.findVirtualOffsetOfFirstRecordInBam(in);
try (BlockCompressedInputStream blockIn = new BlockCompressedInputStream(in)) {
blockIn.seek(recordStart);
// Create a buffer for reading the BAM record lengths. BAM is little-endian.
final ByteBuffer byteBuffer = ByteBuffer.allocate(4).order(ByteOrder.LITTLE_ENDIAN);
final SBIIndexWriter indexWriter = new SBIIndexWriter(out, granularity);
while (true) {
try {
recordStart = blockIn.getFilePointer();
// Read the length of the remainder of the BAM record (`block_size` in the SAM spec)
InputStreamUtils.readFully(blockIn, byteBuffer.array(), 0, 4);
final int blockSize = byteBuffer.getInt(0);
// Process the record start position, then skip to the start of the next BAM record
indexWriter.processRecord(recordStart);
InputStreamUtils.skipFully(blockIn, blockSize);
} catch (RuntimeEOFException e) {
break;
}
}
indexWriter.finish(recordStart, in.length());
}
}
}