/** * Create a CRAMFileReader from either a file or input stream using the reference source returned by * {@link ReferenceSource#getDefaultCRAMReferenceSource() getDefaultCRAMReferenceSource}. * * @param cramFile CRAM file to open * @param inputStream CRAM stream to read * * @throws IllegalArgumentException if the {@code cramFile} and the {@code inputStream} are both null * @throws IllegalStateException if a {@link ReferenceSource#getDefaultCRAMReferenceSource() default} * reference source cannot be acquired */ public CRAMFileReader(final File cramFile, final InputStream inputStream) { this(cramFile, inputStream, ReferenceSource.getDefaultCRAMReferenceSource()); }
/** * Create a CRAMFileReader from either a file or input stream using the reference source returned by * {@link ReferenceSource#getDefaultCRAMReferenceSource() getDefaultCRAMReferenceSource}. * * @param cramFile CRAM file to open * @param inputStream CRAM stream to read * * @throws IllegalArgumentException if the {@code cramFile} and the {@code inputStream} are both null * @throws IllegalStateException if a {@link ReferenceSource#getDefaultCRAMReferenceSource() default} * reference source cannot be acquired */ public CRAMFileReader(final File cramFile, final InputStream inputStream) { this(cramFile, inputStream, ReferenceSource.getDefaultCRAMReferenceSource()); }
} else if (SamStreams.sourceLikeCram(data.asUnbufferedSeekableStream())) { if (referenceSource == null) { referenceSource = ReferenceSource.getDefaultCRAMReferenceSource(); } else if (SamStreams.isCRAMFile(bufferedStream)) { if (referenceSource == null) { referenceSource = ReferenceSource.getDefaultCRAMReferenceSource();
} else if (SamStreams.sourceLikeCram(data.asUnbufferedSeekableStream())) { if (referenceSource == null) { referenceSource = ReferenceSource.getDefaultCRAMReferenceSource(); } else if (SamStreams.isCRAMFile(bufferedStream)) { if (referenceSource == null) { referenceSource = ReferenceSource.getDefaultCRAMReferenceSource();