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); }
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(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, 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(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)); }
.setOption(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, true).open(SamInputResource.of(is));
public ReaderInitializer call() { try { if (threadAllocation.getNumIOThreads() > 0) blockInputStream = new BlockInputStream(dispatcher,readerID,false); SamReaderFactory factory = SamReaderFactory.makeDefault() .validationStringency(validationStringency) .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false); if (SRAAccession.isValid(readerID.getSamFile().getPath())) { reader = factory.open(SamInputResource.of(new SRAAccession(readerID.getSamFile().getPath()))); } else { reader = factory.referenceSequence(referenceFile) .setOption(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, true) .open(readerID.getSamFile()); } } catch ( RuntimeIOException e ) { throw new UserException.CouldNotReadInputFile(readerID.getSamFile(), e); } catch ( SAMFormatException e ) { throw new UserException.MalformedBAM(readerID.getSamFile(), e.getMessage()); } // Picard is throwing a RuntimeException here when BAMs are malformed with bad headers (and so look like SAM files). // Let's keep this separate from the SAMFormatException (which ultimately derives from RuntimeException) case, // just in case we want to change this behavior later. catch ( RuntimeException e ) { throw new UserException.MalformedBAM(readerID.getSamFile(), e.getMessage()); } return this; } }
/** 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(); }
factory.setOption(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES, VALIDATE_INDEX); factory.reapplyOptions(samReader);
factory.setOption(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES, VALIDATE_INDEX); factory.reapplyOptions(samReader);