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/*
* The MIT License
*
* Copyright (c) 2009 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.util.BinaryCodec;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.RuntimeEOFException;
import htsjdk.samtools.util.SortingCollection;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.Arrays;
import static htsjdk.samtools.SAMTag.CG;
/**
* Class for translating between in-memory and disk representation of BAMRecord.
*/
public class BAMRecordCodec implements SortingCollection.Codec {
private final static Log LOG = Log.getInstance(BAMRecordCodec.class);
private final SAMFileHeader header;
private final BinaryCodec binaryCodec = new BinaryCodec();
private final BinaryTagCodec binaryTagCodec = new BinaryTagCodec(binaryCodec);
private final SAMRecordFactory samRecordFactory;
private boolean isReferenceSizeWarningShowed = false;
public BAMRecordCodec(final SAMFileHeader header) {
this(header, new DefaultSAMRecordFactory());
}
public BAMRecordCodec(final SAMFileHeader header, final SAMRecordFactory factory) {
this.header = header;
this.samRecordFactory = factory;
}
@Override
public BAMRecordCodec clone() {
// Do not clone the references to codecs, as they must be distinct for each instance.
return new BAMRecordCodec(this.header, this.samRecordFactory);
}
/**
* Sets the output stream that records will be written to.
*/
@Override
public void setOutputStream(final OutputStream os) {
this.binaryCodec.setOutputStream(os);
}
/**
* Sets the output stream that records will be written to.
*/
public void setOutputStream(final OutputStream os, final String filename) {
this.binaryCodec.setOutputStream(os);
this.binaryCodec.setOutputFileName(filename);
}
/**
* Sets the input stream that records will be read from.
*/
@Override
public void setInputStream(final InputStream is) {
this.binaryCodec.setInputStream(is);
}
/**
* Sets the input stream that records will be read from.
*/
public void setInputStream(final InputStream is, final String filename) {
this.binaryCodec.setInputStream(is);
this.binaryCodec.setInputFileName(filename);
}
/**
* Write object to OutputStream.
* Reference and mate reference indices must be resolvable, which either means that these have been set into the
* SAMRecord directly, or the SAMRecord must have a header assigned into it so that reference names can be
* resolved into indices.
*
* @param alignment Record to be written.
*/
@Override
public void encode(final SAMRecord alignment) {
// Compute block size, as it is the first element of the file representation of SAMRecord
final int readLength = alignment.getReadLength();
// If cigar is too long, put into CG tag and replace with sentinel value.
// Using alignment.getCigarLength() here causes problems, so access the cigar instead
final Cigar cigarToWrite;
final boolean cigarSwitcharoo = alignment.getCigar().numCigarElements() > BAMRecord.MAX_CIGAR_OPERATORS;
if (cigarSwitcharoo) {
final int[] cigarEncoding = BinaryCigarCodec.encode(alignment.getCigar());
alignment.setAttribute(CG.name(), cigarEncoding);
cigarToWrite = makeSentinelCigar(alignment.getCigar());
}
else {
cigarToWrite = alignment.getCigar();
}
int blockSize = BAMFileConstants.FIXED_BLOCK_SIZE + alignment.getReadNameLength() + 1 + // null terminated
cigarToWrite.numCigarElements() * BAMRecord.CIGAR_SIZE_MULTIPLIER +
(readLength + 1) / 2 + // 2 bases per byte, round up
readLength;
final int attributesSize = alignment.getAttributesBinarySize();
if (attributesSize != -1) {
// binary attribute size already known, don't need to compute.
blockSize += attributesSize;
} else {
SAMBinaryTagAndValue attribute = alignment.getBinaryAttributes();
while (attribute != null) {
blockSize += (BinaryTagCodec.getTagSize(attribute.value));
attribute = attribute.getNext();
}
}
// shouldn't interact with the long-cigar above since the Sentinel Cigar has the same referenceLength as
// the actual cigar.
int indexBin = 0;
if (alignment.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START) {
if (!warnIfReferenceIsTooLargeForBinField(alignment)) {
indexBin = alignment.computeIndexingBin();
}
}
// Blurt out the elements
this.binaryCodec.writeInt(blockSize);
this.binaryCodec.writeInt(alignment.getReferenceIndex());
// 0-based!!
this.binaryCodec.writeInt(alignment.getAlignmentStart() - 1);
this.binaryCodec.writeUByte((short) (alignment.getReadNameLength() + 1));
this.binaryCodec.writeUByte((short) alignment.getMappingQuality());
this.binaryCodec.writeUShort(indexBin);
this.binaryCodec.writeUShort(cigarToWrite.numCigarElements());
this.binaryCodec.writeUShort(alignment.getFlags());
this.binaryCodec.writeInt(alignment.getReadLength());
this.binaryCodec.writeInt(alignment.getMateReferenceIndex());
this.binaryCodec.writeInt(alignment.getMateAlignmentStart() - 1);
this.binaryCodec.writeInt(alignment.getInferredInsertSize());
final byte[] variableLengthBinaryBlock = alignment.getVariableBinaryRepresentation();
if (variableLengthBinaryBlock != null) {
// Don't need to encode variable-length block, because it is unchanged from
// when the record was read from a BAM file.
this.binaryCodec.writeBytes(variableLengthBinaryBlock);
} else {
if (alignment.getReadLength() != alignment.getBaseQualities().length &&
alignment.getBaseQualities().length != 0) {
throw new RuntimeException("Mismatch between read length and quals length writing read " +
alignment.getReadName() + "; read length: " + alignment.getReadLength() +
"; quals length: " + alignment.getBaseQualities().length);
}
this.binaryCodec.writeString(alignment.getReadName(), false, true);
final int[] binaryCigar = BinaryCigarCodec.encode(cigarToWrite);
for (final int cigarElement : binaryCigar) {
// Assumption that this will fit into an integer, despite the fact
// that it is spec'ed as a uint.
this.binaryCodec.writeInt(cigarElement);
}
try {
this.binaryCodec.writeBytes(SAMUtils.bytesToCompressedBases(alignment.getReadBases()));
} catch (final IllegalArgumentException ex) {
final String msg = ex.getMessage() + " in read: " + alignment.getReadName();
throw new IllegalStateException(msg, ex);
}
byte[] qualities = alignment.getBaseQualities();
if (qualities.length == 0) {
qualities = new byte[alignment.getReadLength()];
Arrays.fill(qualities, (byte) 0xFF);
}
this.binaryCodec.writeBytes(qualities);
SAMBinaryTagAndValue attribute = alignment.getBinaryAttributes();
while (attribute != null) {
this.binaryTagCodec.writeTag(attribute.tag, attribute.value, attribute.isUnsignedArray());
attribute = attribute.getNext();
}
}
if (cigarSwitcharoo) {
alignment.setAttribute(CG.name(), null);
}
}
/**
* Create a "Sentinel" cigar that will be placed in BAM file when the actual cigar has more than 0xffff operator,
* which are not supported by the bam format. The actual cigar will be encoded and placed in the CG attribute.
* @param cigar actual cigar to create sentinel cigar for
* @return sentinel cigar xSyN with readLength (x) and referenceLength (y) matching the input cigar.
*/
public static Cigar makeSentinelCigar(final Cigar cigar) {
// in BAM there are only 28 bits for a cigar operator, so this a protection against overflow.
if (cigar.getReadLength() > BAMRecord.MAX_CIGAR_ELEMENT_LENGTH) {
throw new IllegalArgumentException(
String.format(
"Cannot encode (to BAM) a record with more than %d cigar operations and a read-length greater than %d.",
BAMRecord.MAX_CIGAR_OPERATORS, BAMRecord.MAX_CIGAR_ELEMENT_LENGTH));
}
if (cigar.getReferenceLength() > BAMRecord.MAX_CIGAR_ELEMENT_LENGTH) {
throw new IllegalArgumentException(
String.format(
"Cannot encode (to BAM) a record that has than %d cigar operations and spans more than %d bases on the reference.",
BAMRecord.MAX_CIGAR_OPERATORS, BAMRecord.MAX_CIGAR_ELEMENT_LENGTH));
}
return new Cigar(Arrays.asList(
new CigarElement(cigar.getReadLength(), CigarOperator.S),
new CigarElement(cigar.getReferenceLength(), CigarOperator.N)));
}
/** Emits a warning the first time a reference too large for binning indexing is encountered.
*
* @param rec the SAMRecord to examine
* @return true if the sequence is too large, false otherwise
*/
private boolean warnIfReferenceIsTooLargeForBinField(final SAMRecord rec) {
final SAMSequenceRecord sequence = rec.getHeader() != null ? rec.getHeader().getSequence(rec.getReferenceName()) : null;
final boolean tooLarge = sequence != null && SAMUtils.isReferenceSequenceIncompatibleWithBAI(sequence);
if (!isReferenceSizeWarningShowed && tooLarge && rec.getValidationStringency() != ValidationStringency.SILENT) {
LOG.warn("Reference length is too large for BAM bin field.");
LOG.warn("Reads on references longer than " + GenomicIndexUtil.BIN_GENOMIC_SPAN + "bp will have bin set to 0.");
isReferenceSizeWarningShowed = true;
}
return tooLarge;
}
/**
* Read the next record from the input stream and convert into a java object.
*
* @return null if no more records. Should throw exception if EOF is encountered in the middle of
* a record.
*/
@Override
public SAMRecord decode() {
final int recordLength;
try {
recordLength = this.binaryCodec.readInt();
} catch (final RuntimeEOFException e) {
return null;
}
if (recordLength < BAMFileConstants.FIXED_BLOCK_SIZE) {
throw new SAMFormatException("Invalid record length: " + recordLength);
}
final int referenceID = this.binaryCodec.readInt();
final int coordinate = this.binaryCodec.readInt() + 1;
final short readNameLength = this.binaryCodec.readUByte();
final short mappingQuality = this.binaryCodec.readUByte();
final int bin = this.binaryCodec.readUShort();
final int cigarLen = this.binaryCodec.readUShort();
final int flags = this.binaryCodec.readUShort();
final int readLen = this.binaryCodec.readInt();
final int mateReferenceID = this.binaryCodec.readInt();
final int mateCoordinate = this.binaryCodec.readInt() + 1;
final int insertSize = this.binaryCodec.readInt();
final byte[] restOfRecord = new byte[recordLength - BAMFileConstants.FIXED_BLOCK_SIZE];
this.binaryCodec.readBytes(restOfRecord);
final BAMRecord ret = this.samRecordFactory.createBAMRecord(
header, referenceID, coordinate, readNameLength, mappingQuality,
bin, cigarLen, flags, readLen, mateReferenceID, mateCoordinate, insertSize, restOfRecord);
if (null != header) {
// don't reset a null header as this will clobber the reference and mate reference indices
ret.setHeader(header);
}
return ret;
}
}
