/** * Sorts the internal collection of intervals by coordinate. * * Note: this function modifies the object in-place and is therefore difficult to work with. * * @deprecated use {@link #sorted()} instead. */ @Deprecated public void sort() { Collections.sort(this.intervals, new IntervalCoordinateComparator(this.header)); this.header.setSortOrder(SAMFileHeader.SortOrder.coordinate); }
/** * Sorts the internal collection of intervals by coordinate. * * Note: this function modifies the object in-place and is therefore difficult to work with. * * @deprecated use {@link #sorted()} instead. */ @Deprecated public void sort() { Collections.sort(this.intervals, new IntervalCoordinateComparator(this.header)); this.header.setSortOrder(SAMFileHeader.SortOrder.coordinate); }
/** Sorts the internal collection of intervals by coordinate. */ @Deprecated // Use sorted() instead of sort(). The sort() function modifies the object in-place and // is therefore difficult to work with. sorted() returns a new IntervalList that is sorted public void sort() { Collections.sort(this.intervals, new IntervalCoordinateComparator(this.header)); this.header.setSortOrder(SAMFileHeader.SortOrder.coordinate); }
/** * returns an independent sorted IntervalList */ public IntervalList sorted() { final IntervalList sorted = IntervalList.copyOf(this); sorted.intervals.sort(new IntervalCoordinateComparator(sorted.header)); sorted.header.setSortOrder(SAMFileHeader.SortOrder.coordinate); return sorted; }
/** * returns an independent sorted IntervalList */ public IntervalList sorted() { final IntervalList sorted = IntervalList.copyOf(this); sorted.intervals.sort(new IntervalCoordinateComparator(sorted.header)); sorted.header.setSortOrder(SAMFileHeader.SortOrder.coordinate); return sorted; }
/** returns an independent sorted IntervalList*/ public IntervalList sorted() { final IntervalList sorted = IntervalList.copyOf(this); Collections.sort(sorted.intervals, new IntervalCoordinateComparator(sorted.header)); sorted.header.setSortOrder(SAMFileHeader.SortOrder.coordinate); return sorted; }
/** * Creates an artificial sam header based on the sequence dictionary dict * * @return a new sam header */ public static SAMFileHeader createArtificialSamHeader(final SAMSequenceDictionary dict) { SAMFileHeader header = new SAMFileHeader(); header.setSortOrder(htsjdk.samtools.SAMFileHeader.SortOrder.coordinate); header.setSequenceDictionary(dict); return header; }
private void initChromosomeChunk(int sampleIdx, int chromosomeChunkIdx) { Logger.debug("Writer init: %d, %d", sampleIdx, chromosomeChunkIdx); samHeaders[sampleIdx].setSortOrder(SortOrder.unsorted); writers[sampleIdx][chromosomeChunkIdx] = writerFactory.makeBAMWriter(samHeaders[sampleIdx], false, new File(getTempFilename(sampleIdx, chromosomeChunkIdx)), TEMP_COMPRESSION_LEVEL); }
@Test(expectedExceptions = SAMException.class) public void testRequireCoordinateSortOrder() { SAMFileHeader header = new SAMFileHeader(); header.setSortOrder(SAMFileHeader.SortOrder.queryname); new BAMIndexer(new ByteArrayOutputStream(), header); }
@Test(expectedExceptions = SAMException.class) public void testRequireCoordinateSortOrder() { SAMFileHeader header = new SAMFileHeader(); header.setSortOrder(SAMFileHeader.SortOrder.queryname); new CRAMCRAIIndexer(new ByteArrayOutputStream(), header); }
private SAMFileHeader createOutHeader( final SAMFileHeader inHeader, final SAMFileHeader.SortOrder sortOrder, final boolean removeAlignmentInformation) { final SAMFileHeader outHeader = new SAMFileHeader(); outHeader.setSortOrder(sortOrder); if (!removeAlignmentInformation) { outHeader.setSequenceDictionary(inHeader.getSequenceDictionary()); outHeader.setProgramRecords(inHeader.getProgramRecords()); } return outHeader; }
private SAMFileHeader createOutHeader( final SAMFileHeader inHeader, final SAMFileHeader.SortOrder sortOrder, final boolean removeAlignmentInformation) { final SAMFileHeader outHeader = new SAMFileHeader(); outHeader.setSortOrder(sortOrder); if (!removeAlignmentInformation) { outHeader.setSequenceDictionary(inHeader.getSequenceDictionary()); outHeader.setProgramRecords(inHeader.getProgramRecords()); } return outHeader; }
public static SAMFileHeader duplicateSAMFileHeader(SAMFileHeader toCopy) { SAMFileHeader copy = new SAMFileHeader(); copy.setSortOrder(toCopy.getSortOrder()); copy.setGroupOrder(toCopy.getGroupOrder()); copy.setProgramRecords(toCopy.getProgramRecords()); copy.setReadGroups(toCopy.getReadGroups()); copy.setSequenceDictionary(toCopy.getSequenceDictionary()); for (Map.Entry<String, String> e : toCopy.getAttributes()) copy.setAttribute(e.getKey(), e.getValue()); return copy; }
protected void kickedFromCache(FastqRead read) { if (writer == null) { log.info("Creating overflow BAM file."); headerForOverflowWriter = header.clone(); headerForOverflowWriter.setSortOrder(SAMFileHeader.SortOrder.queryname); writer = new SAMFileWriterFactory().makeBAMWriter(headerForOverflowWriter, false, cacheOverFlowStream); } SAMRecord r = read.toSAMRecord(writer.getFileHeader()); writer.addAlignment(r); }
private SAMFileHeader createSAMHeader(SAMFileHeader.SortOrder sortOrder) { final SAMFileHeader header = new SAMFileHeader(); header.setSortOrder(sortOrder); header.addSequence(new SAMSequenceRecord("chr1", 123)); SAMReadGroupRecord readGroupRecord = new SAMReadGroupRecord("1"); header.addReadGroup(readGroupRecord); return header; }
@Test public void testContigHasColon() { SAMFileHeader header = new SAMFileHeader(); header.setSortOrder(htsjdk.samtools.SAMFileHeader.SortOrder.coordinate); SAMSequenceDictionary dict = new SAMSequenceDictionary(); SAMSequenceRecord rec = new SAMSequenceRecord("c:h:r1", 10); rec.setSequenceLength(10); dict.addSequence(rec); header.setSequenceDictionary(dict); final GenomeLocParser myGenomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); GenomeLoc loc = myGenomeLocParser.parseGenomeLoc("c:h:r1:4-5"); assertEquals(0, loc.getContigIndex()); assertEquals(loc.getStart(), 4); assertEquals(loc.getStop(), 5); }
private SAMFileHeader createSAMHeader(SAMFileHeader.SortOrder sortOrder) { final SAMFileHeader header = new SAMFileHeader(); header.setSortOrder(sortOrder); header.addSequence(new SAMSequenceRecord("chr1", 123)); header.addSequence(new SAMSequenceRecord("chr2", 123)); SAMReadGroupRecord readGroupRecord = new SAMReadGroupRecord("1"); header.addReadGroup(readGroupRecord); return header; }
private SAMFileWriterFactory createWriterFactoryWithOptions(SAMFileHeader header) { final SAMFileWriterFactory factory = new SAMFileWriterFactory(); factory.setCreateIndex(true); factory.setCreateMd5File(true); // index only created if coordinate sorted header.setSortOrder(SAMFileHeader.SortOrder.coordinate); header.addSequence(new SAMSequenceRecord("chr1", 123)); header.addReadGroup(new SAMReadGroupRecord("1")); return factory; }
private void createSmallBam(final Path outputPath) { final SAMFileWriterFactory factory = new SAMFileWriterFactory(); factory.setCreateIndex(true); factory.setCreateMd5File(true); final SAMFileHeader header = new SAMFileHeader(); // index only created if coordinate sorted header.setSortOrder(SAMFileHeader.SortOrder.coordinate); header.addSequence(new SAMSequenceRecord("chr1", 123)); try (final SAMFileWriter writer = factory.makeBAMWriter(header, false, outputPath)) { fillSmallBam(writer); } }
private void createSmallBam(final File outputFile) { final SAMFileWriterFactory factory = new SAMFileWriterFactory(); factory.setCreateIndex(true); factory.setCreateMd5File(true); final SAMFileHeader header = new SAMFileHeader(); // index only created if coordinate sorted header.setSortOrder(SAMFileHeader.SortOrder.coordinate); header.addSequence(new SAMSequenceRecord("chr1", 123)); try (final SAMFileWriter writer = factory.makeBAMWriter(header, false, outputFile)) { fillSmallBam(writer); } }