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/*
* The MIT License
*
* Copyright (c) 2014 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.variant.utils;
import htsjdk.samtools.*;
import htsjdk.samtools.cram.build.CramIO;
import htsjdk.samtools.cram.structure.Container;
import htsjdk.samtools.cram.structure.CramHeader;
import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
import htsjdk.samtools.util.*;
import htsjdk.tribble.util.ParsingUtils;
import htsjdk.variant.vcf.VCFFileReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Arrays;
import java.util.Collection;
import java.util.Optional;
/**
* Small class for loading a SAMSequenceDictionary from a file
* @author farjoun on 2/25/2014
*/
public class SAMSequenceDictionaryExtractor {
enum TYPE {
FASTA(FileExtensions.FASTA) {
@Override
SAMSequenceDictionary extractDictionary(final Path reference) {
final SAMSequenceDictionary dict = ReferenceSequenceFileFactory.getReferenceSequenceFile(reference).getSequenceDictionary();
if (dict == null)
throw new SAMException("Could not find dictionary next to reference file " + reference.toUri().toString());
return dict;
}
},
DICTIONARY(FileExtensions.DICT) {
@Override
SAMSequenceDictionary extractDictionary(final Path dictionary) {
try (BufferedLineReader bufferedLineReader =
new BufferedLineReader(ParsingUtils.openInputStream(dictionary.toUri().toString()))) {
final SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
final SAMFileHeader header = codec.decode(bufferedLineReader, dictionary.toString());
return header.getSequenceDictionary();
} catch (final IOException e) {
throw new SAMException("Could not open sequence dictionary file: " + dictionary, e);
}
}
},
CRAM(FileExtensions.CRAM) {
@Override
SAMSequenceDictionary extractDictionary(final Path cramPath) {
IOUtil.assertFileIsReadable(cramPath);
try (final InputStream in = Files.newInputStream(cramPath)) {
final CramHeader cramHeader = CramIO.readCramHeader(in);
final Optional samHeader = Optional.ofNullable(
Container.readSAMFileHeaderContainer(cramHeader.getCRAMVersion(), in, cramPath.toString()));
if (samHeader.isPresent()) {
return samHeader.get().getSequenceDictionary();
}
} catch (IOException e) {
throw new RuntimeIOException(e);
}
throw new SAMException(String.format("Can't retrieve sequence dictionary from %s", cramPath));
}
},
SAM(FileExtensions.SAM, FileExtensions.BAM) {
@Override
SAMSequenceDictionary extractDictionary(final Path sam) {
return SamReaderFactory.makeDefault().getFileHeader(sam).getSequenceDictionary();
}
},
VCF(FileExtensions.VCF_LIST.toArray(new String[0])) {
@Override
SAMSequenceDictionary extractDictionary(final Path vcf) {
try (VCFFileReader vcfPathReader = new VCFFileReader(vcf, false)){
return vcfPathReader.getFileHeader().getSequenceDictionary();
}
}
},
INTERVAL_LIST(FileExtensions.INTERVAL_LIST, FileExtensions.COMPRESSED_INTERVAL_LIST) {
@Override
SAMSequenceDictionary extractDictionary(final Path intervalList) {
return IntervalList.fromPath(intervalList).getHeader().getSequenceDictionary();
}
};
final Collection applicableExtensions;
TYPE(final String... s) {
applicableExtensions = CollectionUtil.makeSet(s);
}
TYPE(final Collection extensions) {
applicableExtensions = extensions;
}
/**
* @deprecated in favor of {@link VCFFileReader##extractDictionary(Path) }
* */
@Deprecated
SAMSequenceDictionary extractDictionary(final File file) {return extractDictionary(file.toPath());}
abstract SAMSequenceDictionary extractDictionary(final Path file);
/**
* @deprecated in favor of {@link SAMSequenceDictionaryExtractor##forFile(Path) }
*/
@Deprecated
static TYPE forFile(final File dictionaryExtractable) {
return forFile(dictionaryExtractable.toPath());
}
static TYPE forFile(final Path dictionaryExtractable) {
for (final TYPE type : TYPE.values()) {
for (final String s : type.applicableExtensions) {
if (dictionaryExtractable.toUri().toString().endsWith(s)) {
return type;
}
}
}
throw new SAMException("Cannot figure out type of file " + dictionaryExtractable.toUri().toString() + " from extension. Current implementation understands the following types: " + Arrays.toString(TYPE.values()));
}
@Override
public String toString() {
return super.toString() + ": " + applicableExtensions.toString();
}
}
/**
* @deprecated in favor of {@link SAMSequenceDictionaryExtractor#extractDictionary(Path) }
*/
@Deprecated
public static SAMSequenceDictionary extractDictionary(final File file) {
return extractDictionary(file.toPath());
}
public static SAMSequenceDictionary extractDictionary(final Path path) {
return TYPE.forFile(path).extractDictionary(path);
}
}
