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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.reference;
import htsjdk.samtools.SAMException;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SAMTextHeaderCodec;
import htsjdk.samtools.util.BufferedLineReader;
import htsjdk.samtools.util.FileExtensions;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Lazy;
import java.io.File;
import java.io.InputStream;
import java.io.Serializable;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.function.Supplier;
/**
* Provide core sequence dictionary functionality required by all fasta file readers.
* @author Matt Hanna
*/
abstract class AbstractFastaSequenceFile implements ReferenceSequenceFile {
private final Path path;
private final String source;
private final Lazy dictionary;
/**
* Finds and loads the sequence file dictionary.
* @param file Fasta file to read. Also acts as a prefix for supporting files.
*/
AbstractFastaSequenceFile(final File file) {
this(IOUtil.toPath(file));
}
/**
* Finds and loads the sequence file dictionary.
* @param path Fasta file to read. Also acts as a prefix for supporting files.
*/
AbstractFastaSequenceFile(final Path path) {
this.path = path;
this.source = path == null ? "unknown" : path.toAbsolutePath().toString();
// ensure lambda is serializable (by Kryo, when used with Spark)
this.dictionary = new Lazy<>((Supplier & Serializable) (() -> findAndLoadSequenceDictionary(path)));
}
/**
* Constructs an {@link AbstractFastaSequenceFile} with an optional sequence dictionary.
* @param path Fasta file to read. Also acts as a prefix for supporting files.
* @param source Named source used for error messages.
* @param sequenceDictionary The sequence dictionary, or null if there isn't one.
*/
AbstractFastaSequenceFile(final Path path, final String source, final SAMSequenceDictionary sequenceDictionary) {
this.path = path;
this.source = source;
// ensure lambda is serializable (by Kryo, when used with Spark)
this.dictionary = new Lazy<>((Supplier & Serializable) (() -> sequenceDictionary));
}
/** Attempts to find and load the sequence dictionary if present. */
protected SAMSequenceDictionary findAndLoadSequenceDictionary(final Path fasta) {
final Path dictPath = findSequenceDictionary(path);
if (dictPath == null) return null;
IOUtil.assertFileIsReadable(dictPath);
try (InputStream dictionaryIn = IOUtil.openFileForReading(dictPath)) {
return ReferenceSequenceFileFactory.loadDictionary(dictionaryIn);
}
catch (Exception e) {
throw new SAMException("Could not open sequence dictionary file: " + dictPath, e);
}
}
/** @deprecated use findSequenceDictionary(Path) instead. */
@Deprecated protected static File findSequenceDictionary(final File file) {
final Path dict = findSequenceDictionary(file.toPath());
return dict == null ? null : dict.toFile();
}
/** Attempts to locate the sequence dictionary file adjacent to the reference fasta file. */
protected static Path findSequenceDictionary(final Path fastaPath) {
if (fastaPath == null) {
return null;
}
// Try and locate the dictionary with the default method
final Path dictionary = ReferenceSequenceFileFactory.getDefaultDictionaryForReferenceSequence(fastaPath);
if (Files.exists(dictionary)) {
return dictionary;
}
// try without removing the file extension
final Path dictionaryExt = fastaPath.resolveSibling(fastaPath.getFileName().toString() + FileExtensions.DICT);
if (Files.exists(dictionaryExt)) {
return dictionaryExt;
}
else {
return null;
}
}
/** Returns the path to the reference file. */
protected Path getPath() {
return path;
}
/** Returns the named source of the reference file. */
protected String getSource() {
return source;
}
/**
* Returns the list of sequence records associated with the reference sequence if found
* otherwise null.
*/
@Override
public SAMSequenceDictionary getSequenceDictionary() {
return this.dictionary.get();
}
/** Returns the full path to the reference file. */
protected String getAbsolutePath() {
if (path == null) {
return null;
}
return path.toAbsolutePath().toString();
}
/** Returns the full path to the reference file, or the source if no path was specified. */
public String toString() {
return source;
}
/** default implementation -- override if index is supported */
@Override
public boolean isIndexed() {return false;}
/** default implementation -- override if index is supported */
@Override
public ReferenceSequence getSequence( String contig ) {
throw new UnsupportedOperationException("Index does not appear to exist for " + getSource() + ". samtools faidx can be used to create an index");
}
/** default implementation -- override if index is supported */
@Override
public ReferenceSequence getSubsequenceAt( String contig, long start, long stop ) {
throw new UnsupportedOperationException("Index does not appear to exist for " + getSource() + ". samtools faidx can be used to create an index");
}
}
