@Override public ReferenceSequence nextSequence() { SAMSequenceRecord sequence = sequenceRecordIterator.next(); return getSubsequenceAt(sequence.getSequenceName(), 1L, sequence.getSequenceLength()); }
/** * @param acc accession */ public SRAIndexedSequenceFile(SRAAccession acc) { this.acc = acc; if (!acc.isValid()) { throw new RuntimeException("Passed an invalid SRA accession into SRA reader: " + acc); } try { run = gov.nih.nlm.ncbi.ngs.NGS.openReadCollection(acc.toString()); sequenceDictionary = loadSequenceDictionary(); } catch (final ErrorMsg e) { throw new RuntimeException(e); } reset(); }
return new SRAIndexedSequenceFile(new SRAAccession(fastaFile.getPath()));
@Test(dataProvider = "testReferenceMt") public void testReferenceMt(String acc, List<TestReferenceMtData> parallelTests) throws Exception { final ReferenceSequenceFile refSeqFile = new SRAIndexedSequenceFile(new SRAAccession(acc)); final long timeout = 1000L * 5; // just in case final List<Thread> threads = new ArrayList<Thread>(parallelTests.size());
@Test(dataProvider = "testReference") public void testReference(String acc, String refContig, int refStart, int refStop, String refBases) { final ReferenceSequenceFile refSeqFile = new SRAIndexedSequenceFile(new SRAAccession(acc)); final ReferenceSequence refSeq = refSeqFile.getSubsequenceAt(refContig, refStart, refStop); Assert.assertEquals(new String(refSeq.getBases()), refBases); }
/** * @param acc accession */ public SRAIndexedSequenceFile(SRAAccession acc) { this.acc = acc; if (!acc.isValid()) { throw new RuntimeException("Passed an invalid SRA accession into SRA reader: " + acc); } try { run = gov.nih.nlm.ncbi.ngs.NGS.openReadCollection(acc.toString()); sequenceDictionary = loadSequenceDictionary(); } catch (final ErrorMsg e) { throw new RuntimeException(e); } reset(); }
@Override public ReferenceSequence nextSequence() { SAMSequenceRecord sequence = sequenceRecordIterator.next(); return getSubsequenceAt(sequence.getSequenceName(), 1L, sequence.getSequenceLength()); }
ref = new SRAIndexedSequenceFile(new SRAAccession(referenceFile.getPath())); } else { ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(referenceFile);
@Override public ReferenceSequence getSequence(String contig) { return getSubsequenceAt(contig, 1L, sequenceDictionary.getSequence(contig).getSequenceLength()); }
@Override public ReferenceSequence getSequence(String contig) { return getSubsequenceAt(contig, 1L, sequenceDictionary.getSequence(contig).getSequenceLength()); }