Java Code Examples for htsjdk.samtools.reference.ReferenceSequenceFileFactory#getDefaultDictionaryForReferenceSequence()
The following examples show how to use
htsjdk.samtools.reference.ReferenceSequenceFileFactory#getDefaultDictionaryForReferenceSequence() .
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Example 1
Source File: GATKSparkTool.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
/** * Register the reference file (and associated dictionary and index) to be downloaded to every node using Spark's * copying mechanism ({@code SparkContext#addFile()}). * @param ctx the Spark context * @param referencePath the reference file, can be a local file or a remote path * @return the reference file name; the absolute path of the file can be found by a Spark task using {@code SparkFiles#get()} */ protected static String addReferenceFilesForSpark(JavaSparkContext ctx, Path referencePath) { if (referencePath == null) { return null; } Path indexPath = ReferenceSequenceFileFactory.getFastaIndexFileName(referencePath); Path dictPath = ReferenceSequenceFileFactory.getDefaultDictionaryForReferenceSequence(referencePath); Path gziPath = GZIIndex.resolveIndexNameForBgzipFile(referencePath); ctx.addFile(referencePath.toUri().toString()); if (Files.exists(indexPath)) { ctx.addFile(indexPath.toUri().toString()); } if (Files.exists(dictPath)) { ctx.addFile(dictPath.toUri().toString()); } if (Files.exists(gziPath)) { ctx.addFile(gziPath.toUri().toString()); } return referencePath.getFileName().toString(); }
Example 2
Source File: CreateSequenceDictionary.java From picard with MIT License | 5 votes |
/** * Use reference filename to create URI to go into header if URI was not passed on cmd line. */ protected String[] customCommandLineValidation() { if (URI == null) { URI = "file:" + referenceSequence.getReferenceFile().getAbsolutePath(); } if (OUTPUT == null) { OUTPUT = ReferenceSequenceFileFactory.getDefaultDictionaryForReferenceSequence(referenceSequence.getReferenceFile()); logger.info("Output dictionary will be written in ", OUTPUT); } return super.customCommandLineValidation(); }
Example 3
Source File: CachingIndexedFastaSequenceFile.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
/** * Performing several preliminary checks on the file path. * * @param fastaPath Fasta file to be used as reference * @throws UserException If the given {@code fastaPath} is not good. */ private static void checkFastaPath(final Path fastaPath) { // does the fasta file exist? check that first... if (!Files.exists(fastaPath)) { throw new UserException.MissingReference("The specified fasta file (" + fastaPath.toUri() + ") does not exist."); } //this is the .fai index, not the .gzi final Path indexPath = ReferenceSequenceFileFactory.getFastaIndexFileName(fastaPath); // determine the name for the dict file final Path dictPath = ReferenceSequenceFileFactory.getDefaultDictionaryForReferenceSequence(fastaPath); // It's an error if either the fai or dict file does not exist. The user is now responsible // for creating these files. if (!Files.exists(indexPath)) { throw new UserException.MissingReferenceFaiFile(indexPath, fastaPath); } if (!Files.exists(dictPath)) { throw new UserException.MissingReferenceDictFile(dictPath, fastaPath); } //Block-compressed fastas additionally require a gzi index try { final Path gziPath = GZIIndex.resolveIndexNameForBgzipFile(fastaPath); if( IOUtil.isBlockCompressed(fastaPath, true) && !Files.exists(gziPath)){ throw new UserException.MissingReferenceGziFile(gziPath, fastaPath); } } catch (IOException e) { throw new UserException.CouldNotReadInputFile("Couldn't open fasta file: " + fastaPath.toUri().toString() + ".", e); } }
Example 4
Source File: CreateSequenceDictionary.java From varsim with BSD 2-Clause "Simplified" License | 5 votes |
public CreateSequenceDictionary(String FastaSequenceFileName) { try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new RuntimeException("MD5 algorithm not found", e); } REFERENCE_SEQUENCE = new File(FastaSequenceFileName); URI = "file:" + REFERENCE_SEQUENCE.getAbsolutePath(); OUTPUT = ReferenceSequenceFileFactory.getDefaultDictionaryForReferenceSequence(REFERENCE_SEQUENCE); logger.info("Output dictionary will be written in ", OUTPUT); doWork(); }