public static void main(String[] args) throws IOException { if (args.length < 2) { System.err.println( "Usage: GetSortedBAMHeader input output\n\n"+ "Reads the BAM header from input (a standard BGZF-compressed BAM "+ "file), and\nwrites it (BGZF-compressed, no terminator block) to "+ "output. Sets the sort order\nindicated in the SAM header to "+ "'coordinate'."); System.exit(1); } final SAMFileHeader h = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT) .setUseAsyncIo(false) .open(new File(args[0])).getFileHeader(); h.setSortOrder(SAMFileHeader.SortOrder.coordinate); new SAMOutputPreparer().prepareForRecords( new FileOutputStream(args[1]), SAMFormat.BAM, h); } }
public static void main(String[] args) throws IOException { if (args.length < 2) { System.err.println( "Usage: GetSortedBAMHeader input output\n\n"+ "Reads the BAM header from input (a standard BGZF-compressed BAM "+ "file), and\nwrites it (BGZF-compressed, no terminator block) to "+ "output. Sets the sort order\nindicated in the SAM header to "+ "'coordinate'."); System.exit(1); } final SAMFileHeader h = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT) .setUseAsyncIo(false) .open(new File(args[0])).getFileHeader(); h.setSortOrder(SAMFileHeader.SortOrder.coordinate); try (FileOutputStream stream = new FileOutputStream(args[1])) { new SAMOutputPreparer().prepareForRecords(stream, SAMFormat.BAM, h); } } }
public static void main(String[] args) throws IOException { if (args.length < 2) { System.err.println( "Usage: GetSortedBAMHeader input output\n\n"+ "Reads the BAM header from input (a standard BGZF-compressed BAM "+ "file), and\nwrites it (BGZF-compressed, no terminator block) to "+ "output. Sets the sort order\nindicated in the SAM header to "+ "'coordinate'."); System.exit(1); } final SAMFileHeader h = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT) .setUseAsyncIo(false) .open(new File(args[0])).getFileHeader(); h.setSortOrder(SAMFileHeader.SortOrder.coordinate); try (FileOutputStream stream = new FileOutputStream(args[1])) { new SAMOutputPreparer().prepareForRecords(stream, SAMFormat.BAM, h); } } }
private SamReader createSamReader(InputStream in, ValidationStringency stringency) { SamReaderFactory readerFactory = SamReaderFactory.makeDefault() .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false) .setUseAsyncIo(false); if (stringency != null) { readerFactory.validationStringency(stringency); } return readerFactory.open(SamInputResource.of(in)); }
private SamReader createSamReader(InputStream in, ValidationStringency stringency) { SamReaderFactory readerFactory = SamReaderFactory.makeDefault() .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false) .setUseAsyncIo(false); if (stringency != null) { readerFactory.validationStringency(stringency); } return readerFactory.open(SamInputResource.of(in)); }
private SamReader createSamReader(InputStream in, ValidationStringency stringency) { SamReaderFactory readerFactory = SamReaderFactory.makeDefault() .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false) .setUseAsyncIo(false); if (stringency != null) { readerFactory.validationStringency(stringency); } return readerFactory.open(SamInputResource.of(in)); }
private SamReader createSamReader(SeekableStream in, SeekableStream inIndex, ValidationStringency stringency) { SamReaderFactory readerFactory = SamReaderFactory.makeDefault() .setOption(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES, true) .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false) .setUseAsyncIo(false); if (stringency != null) { readerFactory.validationStringency(stringency); } SamInputResource resource = SamInputResource.of(in); if (inIndex != null) { resource.index(inIndex); } return readerFactory.open(resource); }
.setOption(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES, true) .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false) .setUseAsyncIo(false); for (Path bamFile : bamFiles) { FileSystem fs = bamFile.getFileSystem(conf);
.setOption(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES, true) .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false) .setUseAsyncIo(false);
.setOption(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES, true) .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false) .setUseAsyncIo(false);
private SamReader createSamReader(SeekableStream in, SeekableStream inIndex, ValidationStringency stringency, boolean useIntelInflater) { SamReaderFactory readerFactory = SamReaderFactory.makeDefault() .setOption(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES, true) .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false) .setUseAsyncIo(false); if (stringency != null) { readerFactory.validationStringency(stringency); } SamInputResource resource = SamInputResource.of(in); if (inIndex != null) { resource.index(inIndex); } if (useIntelInflater) { readerFactory.inflaterFactory(IntelGKLAccessor.newInflatorFactor()); } return readerFactory.open(resource); }
private SamReader createSamReader(SeekableStream in, SeekableStream inIndex, ValidationStringency stringency, boolean useIntelInflater) { SamReaderFactory readerFactory = SamReaderFactory.makeDefault() .setOption(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES, true) .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false) .setUseAsyncIo(false); if (stringency != null) { readerFactory.validationStringency(stringency); } SamInputResource resource = SamInputResource.of(in); if (inIndex != null) { resource.index(inIndex); } if (useIntelInflater) { readerFactory.inflaterFactory(IntelGKLAccessor.newInflatorFactor()); } return readerFactory.open(resource); }
/** Does not close the stream. */ public static SAMFileHeader readSAMHeaderFrom( final InputStream in, final Configuration conf) { final ValidationStringency stringency = getValidationStringency(conf); SamReaderFactory readerFactory = SamReaderFactory.makeDefault() .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false) .setUseAsyncIo(false); if (stringency != null) { readerFactory.validationStringency(stringency); } final ReferenceSource refSource = getReferenceSource(conf); if (null != refSource) { readerFactory.referenceSource(refSource); } return readerFactory.open(SamInputResource.of(in)).getFileHeader(); }
/** Does not close the stream. */ public static SAMFileHeader readSAMHeaderFromStream( final InputStream in, final Configuration conf) { final ValidationStringency stringency = getValidationStringency(conf); SamReaderFactory readerFactory = SamReaderFactory.makeDefault() .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false) .setUseAsyncIo(false); if (stringency != null) { readerFactory.validationStringency(stringency); } final ReferenceSource refSource = getReferenceSource(conf); if (null != refSource) { readerFactory.referenceSource(refSource); } return readerFactory.open(SamInputResource.of(in)).getFileHeader(); }
/** Does not close the stream. */ public static SAMFileHeader readSAMHeaderFrom( final InputStream in, final Configuration conf) { final ValidationStringency stringency = getValidationStringency(conf); SamReaderFactory readerFactory = SamReaderFactory.makeDefault() .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false) .setUseAsyncIo(false); if (stringency != null) { readerFactory.validationStringency(stringency); } final ReferenceSource refSource = getReferenceSource(conf); if (null != refSource) { readerFactory.referenceSource(refSource); } return readerFactory.open(SamInputResource.of(in)).getFileHeader(); }
SamReader open = SamReaderFactory.makeDefault().setUseAsyncIo(false) .open(SamInputResource.of(inFile)); SAMFileSpan span = open.indexing().getFilePointerSpanningReads();
SamReader open = SamReaderFactory.makeDefault().setUseAsyncIo(false) .open(SamInputResource.of(inFile)); SAMFileSpan span = open.indexing().getFilePointerSpanningReads();
SamReaderFactory .makeDefault() .setUseAsyncIo(false) .open(SamInputResource.of(inFile));
SamReader open = SamReaderFactory.makeDefault().setUseAsyncIo(false) .open(SamInputResource.of(inFile)); SAMFileSpan span = open.indexing().getFilePointerSpanningReads();
SamReader open = SamReaderFactory.makeDefault().setUseAsyncIo(false) .open(SamInputResource.of(inFile)); SAMFileSpan span = open.indexing().getFilePointerSpanningReads();