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Ported GATK's FastaReferenceWriter (#1172)
* - Ported GATK's FastaReferenceWriter - Implemented some basic validation functionality rather than stripping it out of the implementation of FastaReferenceWriter) - Implemented a simple version of a RandomDNA creator (and modified SAMRecordSetBuilder to use it) - Ported the tests (for FastaReferenceWriter) from GATK.
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Yossi Farjoun
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Feb 1, 2019
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src/main/java/htsjdk/samtools/reference/FastaReferenceWriter.java
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src/main/java/htsjdk/samtools/reference/FastaReferenceWriterBuilder.java
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| /* | ||
| * The MIT License | ||
| * | ||
| * Copyright (c) 2018 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. | ||
| */ | ||
|
|
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| package htsjdk.samtools.reference; | ||
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| import htsjdk.utils.ValidationUtils; | ||
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| import java.io.IOException; | ||
| import java.io.OutputStream; | ||
| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
|
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| /** | ||
| * Buider for a {@link htsjdk.samtools.reference.FastaReferenceWriter} | ||
| * <p> | ||
| * You can set each of the three outputs (fasta, dictionary and index) to a file or a stream. | ||
| * by default if you provide a file to the fasta an accompanying index and dictionary will be created. | ||
| * This behaviour can be controlled by {@link #setMakeDictOutput(boolean)} and {@link #setMakeFaiOutput(boolean)} | ||
| * <p> | ||
| * The default bases-per-line is {@value FastaReferenceWriter#DEFAULT_BASES_PER_LINE}. | ||
| * <p> | ||
| * Setting a file or an output stream for any of the three outputs (fasta, index or dict) will invalidate the other | ||
| * output type (i.e. setting a file output will invalidate a previous stream and vice-versa). | ||
| * </p> | ||
| */ | ||
| public class FastaReferenceWriterBuilder { | ||
| private Path fastaFile; | ||
| private boolean makeFaiOutput = true; | ||
| private boolean makeDictOutput = true; | ||
| private int basesPerLine = FastaReferenceWriter.DEFAULT_BASES_PER_LINE; | ||
| private Path indexFile; | ||
| private Path dictFile; | ||
| private OutputStream fastaOutput; | ||
| private OutputStream indexOutput; | ||
| private OutputStream dictOutput; | ||
|
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| private static Path defaultFaiFile(final boolean makeFaiFile, final Path fastaFile) { | ||
| return makeFaiFile ? ReferenceSequenceFileFactory.getFastaIndexFileName(fastaFile) : null; | ||
| } | ||
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| private static Path defaultDictFile(final boolean makeDictFile, final Path fastaFile) { | ||
| return makeDictFile ? ReferenceSequenceFileFactory.getDefaultDictionaryForReferenceSequence(fastaFile) : null; | ||
| } | ||
|
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| protected static int checkBasesPerLine(final int value) { | ||
| ValidationUtils.validateArg(value > 0, "bases per line must be 1 or greater"); | ||
| return value; | ||
| } | ||
|
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| /** | ||
| * Set the output fasta file to write to. Doesn't (currently) support compressed filenames. | ||
| * If the index file and output stream are both null and makeFaiOutput is true (default), a default index file will be created as well. | ||
| * If the dictionary file and output stream are both null and makeDictOutput is true (default), a default dictionary file will be created as well. | ||
| * | ||
| * You can only provide a compressed stream to the fastaOutput, and only in the case that an index isn't written. | ||
| * | ||
| * @param fastaFile a {@link Path} to the output fasta file. | ||
| * @return this builder | ||
| */ | ||
| public FastaReferenceWriterBuilder setFastaFile(final Path fastaFile) { | ||
| this.fastaFile = fastaFile; | ||
| this.fastaOutput = null; | ||
| return this; | ||
| } | ||
|
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| /** | ||
| * Sets whether to automatically generate an index file from the name of the fasta-file (assuming it is given | ||
| * as a file). This can only happen if both the index file and output stream are null. | ||
| * | ||
| * @param makeFaiOutput a boolean flag | ||
| * @return this builder | ||
| */ | ||
| public FastaReferenceWriterBuilder setMakeFaiOutput(final boolean makeFaiOutput) { | ||
| this.makeFaiOutput = makeFaiOutput; | ||
| return this; | ||
| } | ||
|
|
||
| /** | ||
| * Sets whether to automatically generate an dictionary file from the name of the fasta-file (assuming it is given | ||
| * as a file). This can only happen if both the dictionary file and output stream are null. | ||
| * | ||
| * @param makeDictOutput a boolean flag | ||
| * @return this builder | ||
| */ | ||
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| public FastaReferenceWriterBuilder setMakeDictOutput(final boolean makeDictOutput) { | ||
| this.makeDictOutput = makeDictOutput; | ||
| return this; | ||
| } | ||
|
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| /** | ||
| * Sets the number of bases each line of the fasta file will have. | ||
| * the default is {@value FastaReferenceWriter#DEFAULT_BASES_PER_LINE} | ||
| * | ||
| * @param basesPerLine integer (must be positive, validated on {@link #build()}) indicating the number of bases per line in | ||
| * the output | ||
| * @return this builder | ||
| */ | ||
| public FastaReferenceWriterBuilder setBasesPerLine(final int basesPerLine) { | ||
| this.basesPerLine = basesPerLine; | ||
| return this; | ||
| } | ||
|
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| /** | ||
| * Set the output index file to write to. Doesn't (currently) support compressed filenames. | ||
| */ | ||
| public FastaReferenceWriterBuilder setIndexFile(final Path indexFile) { | ||
| this.indexFile = indexFile; | ||
| this.indexOutput = null; | ||
| return this; | ||
| } | ||
|
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| /** | ||
| * Set the output dictionary file to write to. | ||
| */ | ||
| public FastaReferenceWriterBuilder setDictFile(final Path dictFile) { | ||
| this.dictFile = dictFile; | ||
| this.dictOutput = null; | ||
| return this; | ||
| } | ||
|
|
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| /** | ||
| * Set the output stream for writing the reference. Doesn't support compressed streams. | ||
| * | ||
| * @param fastaOutput a {@link OutputStream} for the output fasta file. | ||
| * @return this builder | ||
| */ | ||
|
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| public FastaReferenceWriterBuilder setFastaOutput(final OutputStream fastaOutput) { | ||
| this.fastaOutput = fastaOutput; | ||
| this.fastaFile = null; | ||
| return this; | ||
| } | ||
|
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| /** | ||
| * Set the output stream for writing the index. Doesn't support compressed streams. | ||
| * | ||
| * @param indexOutput a {@link OutputStream} for the output index. | ||
| * @return this builder | ||
| */ | ||
| public FastaReferenceWriterBuilder setIndexOutput(final OutputStream indexOutput) { | ||
| this.indexOutput = indexOutput; | ||
| this.indexFile = null; | ||
| return this; | ||
| } | ||
|
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| /** | ||
| * Set the output stream for writing the dictionary. Doesn't support compressed streams. | ||
| * | ||
| * @param dictOutput a {@link OutputStream} for the output dictionary. | ||
| * @return this builder | ||
| */ | ||
| public FastaReferenceWriterBuilder setDictOutput(final OutputStream dictOutput) { | ||
| this.dictOutput = dictOutput; | ||
| this.dictFile = null; | ||
| return this; | ||
| } | ||
|
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| /** | ||
| * Create the {@link FastaReferenceWriter}. This is were all the validations happen: | ||
| * <ld> | ||
| * <li> | ||
| * -One of fastaFile and fastaOutput must be non-null. | ||
| * </li> | ||
| * <li> | ||
| * -the number of bases-per-line must be positive | ||
| * </li> | ||
| * </ld> | ||
| * | ||
| * @return a {@link FastaReferenceWriter} | ||
| * @throws IOException if trouble opening files | ||
| */ | ||
| public FastaReferenceWriter build() throws IOException { | ||
| if (fastaFile == null && fastaOutput == null) { | ||
| throw new IllegalArgumentException("Both fastaFile and fastaOutput were null. Please set one of them to be non-null."); | ||
| } | ||
| if(fastaFile != null) { | ||
| if (indexFile == null && indexOutput == null) { | ||
| indexFile = defaultFaiFile(makeFaiOutput, fastaFile); | ||
| } else if (indexFile != null && indexOutput != null) { | ||
| throw new IllegalArgumentException("Both indexFile and indexOutput were non-null. Please set one of them to be null."); | ||
| } | ||
| if (dictFile == null && dictOutput == null) { | ||
| dictFile = defaultDictFile(makeDictOutput, fastaFile); | ||
| } else if (dictFile != null && dictOutput != null) { | ||
| throw new IllegalArgumentException("Both dictFile and dictOutput were non-null. Please set one of them to be null."); | ||
| } | ||
| } | ||
| // checkout bases-perline first, so that files are not created if failure; | ||
| checkBasesPerLine(basesPerLine); | ||
|
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| if (fastaFile != null) { | ||
| fastaOutput = Files.newOutputStream(fastaFile); | ||
| } | ||
| if (indexFile != null) { | ||
| indexOutput = Files.newOutputStream(indexFile); | ||
| } | ||
| if (dictFile != null) { | ||
| dictOutput = Files.newOutputStream(dictFile); | ||
| } | ||
|
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| return new FastaReferenceWriter(basesPerLine, fastaOutput, indexOutput, dictOutput); | ||
| } | ||
| } |
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