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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.fastq;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMUtils;
import htsjdk.samtools.util.StringUtil;
import java.io.Serializable;
/**
* Simple representation of a FASTQ record, without any conversion
*/
public class FastqRecord implements Serializable {
private static final long serialVersionUID = 1L;
private final String readName;
private final String readString;
private final String qualityHeader;
private final String baseQualityString;
/**
* Default constructor
*
* @param readName the read name (without {@link FastqConstants#SEQUENCE_HEADER})
* @param readBases the read sequence bases
* @param qualityHeader the quality header (without {@link FastqConstants#SEQUENCE_HEADER})
* @param baseQualities the base quality scores
*/
public FastqRecord(final String readName, final String readBases, final String qualityHeader, final String baseQualities) {
if (readName != null && !readName.isEmpty()) {
this.readName = readName;
} else {
this.readName = null;
}
if (qualityHeader != null && !qualityHeader.isEmpty()) {
this.qualityHeader = qualityHeader;
} else {
this.qualityHeader = null;
}
this.readString = readBases;
this.baseQualityString = baseQualities;
}
/**
* Constructor for byte[] arrays
*
* @param readName the read name (without {@link FastqConstants#SEQUENCE_HEADER})
* @param readBases the read sequence bases as ASCII bytes ACGTN=.
* @param qualityHeader the quality header (without {@link FastqConstants#SEQUENCE_HEADER})
* @param baseQualities the base qualities as binary PHRED scores (not ASCII)
*/
public FastqRecord(final String readName, final byte[] readBases, final String qualityHeader, final byte[] baseQualities) {
this(readName, StringUtil.bytesToString(readBases), qualityHeader, SAMUtils.phredToFastq(baseQualities));
}
/**
* Copy constructor
*
* @param other record to copy
*/
public FastqRecord(final FastqRecord other) {
if (other == null) {
throw new IllegalArgumentException("new FastqRecord(null)");
}
this.readName = other.readName;
this.readString = other.readString;
this.qualityHeader = other.qualityHeader;
this.baseQualityString = other.baseQualityString;
}
/**
* @return the read name
* @deprecated since 02/2017. Use {@link #getReadName()} instead
*/
@Deprecated
public String getReadHeader() {
return getReadName();
}
/**
* Get the read name
*
* @return the read name (may be {@code null}).
*/
public String getReadName() {
return readName;
}
/**
* Get the DNA sequence
*
* @return read sequence as a string of ACGTN= (may be {@code null}).
*/
public String getReadString() {
return readString;
}
/**
* Get the DNA sequence.
*
* @return read sequence as ASCII bytes ACGTN=; {@link SAMRecord#NULL_SEQUENCE} if no bases are present.
*/
public byte[] getReadBases() {
return (readString == null) ? SAMRecord.NULL_SEQUENCE : StringUtil.stringToBytes(readString);
}
/**
* Get the base qualities encoded as a FASTQ string
*
* @return the quality string (may be {@code null}).
*/
public String getBaseQualityString() {
return baseQualityString;
}
/**
* Get the base qualities as binary PHRED scores (not ASCII)
*
* @return the base quality; {@link SAMRecord#NULL_QUALS} if no bases are present.
*/
public byte[] getBaseQualities() {
return (baseQualityString == null) ? SAMRecord.NULL_QUALS : SAMUtils.fastqToPhred(baseQualityString);
}
/**
* Get the read length
*
* @return number of bases in the read
*/
public int getReadLength() {
return (readString == null) ? 0 : readString.length();
}
/**
* Get the base quality header
*
* @return the base quality header (may be {@code null}).
*/
public String getBaseQualityHeader() {
return qualityHeader;
}
/**
* shortcut to getReadString().length()
*
* @deprecated since 02/2017. Use {@link #getReadLength()} instead
*/
@Deprecated
public int length() {
return getReadLength();
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime
* result
+ ((qualityHeader == null) ? 0 : qualityHeader.hashCode());
result = prime * result
+ ((baseQualityString == null) ? 0 : baseQualityString.hashCode());
result = prime * result
+ ((readName == null) ? 0 : readName.hashCode());
result = prime * result + ((readString == null) ? 0 : readString.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
FastqRecord other = (FastqRecord) obj;
if (readString == null) {
if (other.readString != null)
return false;
} else if (!readString.equals(other.readString))
return false;
if (qualityHeader == null) {
if (other.qualityHeader != null)
return false;
} else if (!qualityHeader.equals(other.qualityHeader))
return false;
if (baseQualityString == null) {
if (other.baseQualityString != null)
return false;
} else if (!baseQualityString.equals(other.baseQualityString))
return false;
if (readName == null) {
if (other.readName != null)
return false;
} else if (!readName.equals(other.readName))
return false;
return true;
}
/**
* Returns the record as the String FASTQ format.
* @see FastqEncoder#encode(FastqRecord)
*/
public String toFastQString() {
return FastqEncoder.encode(this);
}
/**
* Returns {@link #toFastQString()}.
*
* WARNING: This method will be changed in the future for a simpler representation of the object.
* For code relying on the formatting as a FASTQ String, please refactor your code to use
* {@link #toFastQString()}.
*/
@Override
public String toString() {
// TODO: this should be change in the future for a simpler and more informative form such as
// TODO: return String.format("%s: %s bp", readName, getReadLength());
return toFastQString();
}
}
