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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.variant.variantcontext.VariantContext;
import java.math.BigInteger;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.regex.Pattern;
/**
* Header information about a reference sequence. Corresponds to @SQ header record in SAM text header.
*/
public class SAMSequenceRecord extends AbstractSAMHeaderRecord implements Cloneable
{
public static final long serialVersionUID = 1L; // AbstractSAMHeaderRecord implements Serializable
public final static int UNAVAILABLE_SEQUENCE_INDEX = -1;
private final String mSequenceName; // Value must be interned() if it's ever set/modified
private int mSequenceIndex = UNAVAILABLE_SEQUENCE_INDEX;
private int mSequenceLength = 0;
public static final String SEQUENCE_NAME_TAG = "SN";
public static final String SEQUENCE_LENGTH_TAG = "LN";
public static final String MD5_TAG = "M5";
public static final String ASSEMBLY_TAG = "AS";
public static final String URI_TAG = "UR";
public static final String SPECIES_TAG = "SP";
public static final String DESCRIPTION_TAG = "DS";
/** If one sequence has this length, and another sequence had a different length, isSameSequence will
* not complain that they are different sequences. */
public static final int UNKNOWN_SEQUENCE_LENGTH = 0;
/**
* This is not a valid sequence name, because it is reserved in the RNEXT field of SAM text format
* to mean "same reference as RNAME field."
*/
public static final String RESERVED_RNEXT_SEQUENCE_NAME = "=";
/* use RESERVED_RNEXT_SEQUENCE_NAME instead. */
@Deprecated
public static final String RESERVED_MRNM_SEQUENCE_NAME = RESERVED_RNEXT_SEQUENCE_NAME;
/**
* The standard tags are stored in text header without type information, because the type of these tags is known.
*/
public static final Set STANDARD_TAGS =
new HashSet<>(Arrays.asList(SEQUENCE_NAME_TAG, SEQUENCE_LENGTH_TAG, ASSEMBLY_TAG, MD5_TAG, URI_TAG, SPECIES_TAG));
// These are the chars matched by \\s.
private static final char[] WHITESPACE_CHARS = {' ', '\t', '\n', '\013', '\f', '\r'}; // \013 is vertical tab
private static final Pattern LEGAL_RNAME_PATTERN = Pattern.compile("[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*");
/**
* @deprecated Use {@link #SAMSequenceRecord(String, int)} instead.
* sequenceLength is required for the object to be considered valid.
*/
@Deprecated
public SAMSequenceRecord(final String name) {
this(name, UNKNOWN_SEQUENCE_LENGTH);
}
public SAMSequenceRecord(final String name, final int sequenceLength) {
if (name != null) {
validateSequenceName(name);
mSequenceName = name.intern();
} else {
mSequenceName = null;
}
mSequenceLength = sequenceLength;
}
public String getSequenceName() { return mSequenceName; }
public int getSequenceLength() { return mSequenceLength; }
public void setSequenceLength(final int value) { mSequenceLength = value; }
public String getAssembly() { return (String) getAttribute(ASSEMBLY_TAG); }
public void setAssembly(final String value) { setAttribute(ASSEMBLY_TAG, value); }
public String getSpecies() { return (String) getAttribute(SPECIES_TAG); }
public void setSpecies(final String value) { setAttribute(SPECIES_TAG, value); }
public String getMd5() { return (String) getAttribute(MD5_TAG); }
public void setMd5(final String value) { setAttribute(MD5_TAG, value); }
public String getDescription() { return getAttribute(DESCRIPTION_TAG);}
public void setDescription(final String value) { setAttribute(DESCRIPTION_TAG, value);}
/**
* @return Index of this record in the sequence dictionary it lives in.
*/
public int getSequenceIndex() { return mSequenceIndex; }
// Private state used only by SAM implementation.
public void setSequenceIndex(final int value) { mSequenceIndex = value; }
/**
* Looser comparison than equals(). We look only at sequence index, sequence length, and MD5 tag value
* (or sequence names, if there is no MD5 tag in either record.
*/
public boolean isSameSequence(final SAMSequenceRecord that) {
if (this == that) return true;
if (that == null) return false;
if (mSequenceIndex != that.mSequenceIndex) return false;
// PIC-439. Allow undefined length.
if (mSequenceLength != UNKNOWN_SEQUENCE_LENGTH && that.mSequenceLength != UNKNOWN_SEQUENCE_LENGTH && mSequenceLength != that.mSequenceLength)
return false;
if (this.getAttribute(SAMSequenceRecord.MD5_TAG) != null && that.getAttribute(SAMSequenceRecord.MD5_TAG) != null) {
final BigInteger thisMd5 = new BigInteger((String)this.getAttribute(SAMSequenceRecord.MD5_TAG), 16);
final BigInteger thatMd5 = new BigInteger((String)that.getAttribute(SAMSequenceRecord.MD5_TAG), 16);
if (!thisMd5.equals(thatMd5)) {
return false;
}
}
else {
if (mSequenceName != that.mSequenceName) return false; // Compare using == since we intern() the Strings
}
return true;
}
@Override
public boolean equals(final Object o) {
if (this == o) return true;
if (!(o instanceof SAMSequenceRecord)) return false;
final SAMSequenceRecord that = (SAMSequenceRecord) o;
if (mSequenceIndex != that.mSequenceIndex) return false;
if (mSequenceLength != that.mSequenceLength) return false;
if (!attributesEqual(that)) return false;
if (mSequenceName != that.mSequenceName) return false; // Compare using == since we intern() the name
return true;
}
@Override
public int hashCode() {
return mSequenceName != null ? mSequenceName.hashCode() : 0;
}
@Override
Set getStandardTags() {
return STANDARD_TAGS;
}
@Override
public final SAMSequenceRecord clone() {
final SAMSequenceRecord ret = new SAMSequenceRecord(this.mSequenceName, this.mSequenceLength);
ret.mSequenceIndex = this.mSequenceIndex;
for (final Map.Entry entry : this.getAttributes()) {
ret.setAttribute(entry.getKey(), entry.getValue());
}
return ret;
}
/**
* Truncate sequence name at first whitespace.
*/
public static String truncateSequenceName(final String sequenceName) {
/*
* Instead of using regex split, do it manually for better performance.
*/
int truncateAt = sequenceName.length();
for (final char c : WHITESPACE_CHARS) {
int index = sequenceName.indexOf(c);
if (index != UNAVAILABLE_SEQUENCE_INDEX && index < truncateAt) {
truncateAt = index;
}
}
return sequenceName.substring(0, truncateAt);
}
/**
* Throw an exception if the sequence name is not valid.
*/
public static void validateSequenceName(final String name) {
if (!LEGAL_RNAME_PATTERN.matcher(name).useAnchoringBounds(true).matches()) {
throw new SAMException(String.format("Sequence name '%s' doesn't match regex: '%s' ", name, LEGAL_RNAME_PATTERN));
}
}
@Override
public String toString() {
return String.format(
"SAMSequenceRecord(name=%s,length=%s,dict_index=%s,assembly=%s)",
getSequenceName(),
getSequenceLength(),
getSequenceIndex(),
getAssembly()
);
}
@Override
public String getSAMString() {
return new SAMTextHeaderCodec().getSQLine(this);
}
}
