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@@ -303,111 +303,106 @@ public SamReader open(final SamInputResource resource) { |
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return reader;
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}
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}
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- switch (type) {
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- case PATH: case SEEKABLE_STREAM: case URL:
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- if (SamStreams.sourceLikeBam(data.asUnbufferedSeekableStream())) {
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- final SeekableStream bufferedIndexStream;
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- if (indexDefined && indexMaybe.asUnbufferedSeekableStream() != null) {
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- bufferedIndexStream = IOUtil.maybeBufferedSeekableStream(indexMaybe.asUnbufferedSeekableStream());
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- } else {
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- // TODO: Throw an exception here? An index _may_ have been provided, but we're ignoring it
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- bufferedIndexStream = null;
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- }
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-
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- primitiveSamReader = new BAMFileReader(
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- IOUtil.maybeBufferedSeekableStream(data.asUnbufferedSeekableStream()),
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- bufferedIndexStream,
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- false,
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- asynchronousIO,
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- validationStringency,
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- this.samRecordFactory,
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- this.inflaterFactory
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- );
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- } else if (SamStreams.sourceLikeCram(data.asUnbufferedSeekableStream())) {
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- if (referenceSource == null) {
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- referenceSource = ReferenceSource.getDefaultCRAMReferenceSource();
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- }
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- SeekableStream bufferedIndexStream = indexDefined ?
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- IOUtil.maybeBufferedSeekableStream(indexMaybe.asUnbufferedSeekableStream()) :
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- null;
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- primitiveSamReader = new CRAMFileReader(
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- IOUtil.maybeBufferedSeekableStream(data.asUnbufferedSeekableStream()),
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- bufferedIndexStream, referenceSource, validationStringency);
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+ if (type == InputResource.Type.SEEKABLE_STREAM || type == InputResource.Type.URL) {
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+ if (SamStreams.sourceLikeBam(data.asUnbufferedSeekableStream())) {
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+ final SeekableStream bufferedIndexStream;
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+ if (indexDefined && indexMaybe.asUnbufferedSeekableStream() != null) {
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+ bufferedIndexStream = IOUtil.maybeBufferedSeekableStream(indexMaybe.asUnbufferedSeekableStream());
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} else {
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- // assume its a SAM file/no index
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- LOG.warn("Unable to detect file format from input URL or stream, assuming SAM format.");
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- primitiveSamReader = new SAMTextReader(
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- IOUtil.toBufferedStream(data.asUnbufferedInputStream()),
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- validationStringency, this.samRecordFactory);
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+ // TODO: Throw an exception here? An index _may_ have been provided, but we're ignoring it
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+ bufferedIndexStream = null;
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}
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- break;
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- case SRA_ACCESSION:
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- primitiveSamReader = new SRAFileReader(data.asSRAAccession());
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- break;
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- case FILE: case INPUT_STREAM:
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- InputStream bufferedStream =
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- IOUtil.maybeBufferInputStream(
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- data.asUnbufferedInputStream(),
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- Math.max(Defaults.BUFFER_SIZE, BlockCompressedStreamConstants.MAX_COMPRESSED_BLOCK_SIZE)
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- );
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- File sourceFile = data.asFile();
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- // calling asFile is safe even if indexMaybe is a Google Cloud Storage bucket
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- // (in that case we just get null)
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- final File indexFile = indexMaybe == null ? null : indexMaybe.asFile();
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- if (SamStreams.isBAMFile(bufferedStream)) {
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- if (sourceFile == null || !sourceFile.isFile()) {
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- // check whether we can seek
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- final SeekableStream indexSeekable = indexMaybe == null ? null : indexMaybe.asUnbufferedSeekableStream();
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- // do not close bufferedStream, it's the same stream we're getting here.
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- SeekableStream sourceSeekable = data.asUnbufferedSeekableStream();
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- if (null == sourceSeekable || null == indexSeekable) {
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- // not seekable.
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- // it's OK that we consumed a bit of the stream already, this ctor expects it.
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- primitiveSamReader = new BAMFileReader(bufferedStream, indexFile, false, asynchronousIO,
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- validationStringency, this.samRecordFactory, this.inflaterFactory);
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- } else {
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- // seekable.
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- // need to return to the beginning because it's the same stream we used earlier
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- // and read a bit from, and that form of the ctor expects the stream to start at 0.
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- sourceSeekable.seek(0);
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- primitiveSamReader = new BAMFileReader(
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- sourceSeekable, indexSeekable, false, asynchronousIO, validationStringency,
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- this.samRecordFactory, this.inflaterFactory);
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- }
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- } else {
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- bufferedStream.close();
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- primitiveSamReader = new BAMFileReader(
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- sourceFile, indexFile, false, asynchronousIO,
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+
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+ primitiveSamReader = new BAMFileReader(
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+ IOUtil.maybeBufferedSeekableStream(data.asUnbufferedSeekableStream()),
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+ bufferedIndexStream,
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+ false,
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+ asynchronousIO,
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+ validationStringency,
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+ this.samRecordFactory,
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+ this.inflaterFactory
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+ );
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+ } else if (SamStreams.sourceLikeCram(data.asUnbufferedSeekableStream())) {
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+ if (referenceSource == null) {
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+ referenceSource = ReferenceSource.getDefaultCRAMReferenceSource();
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+ }
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+ SeekableStream bufferedIndexStream = indexDefined ?
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+ IOUtil.maybeBufferedSeekableStream(indexMaybe.asUnbufferedSeekableStream()) :
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+ null;
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+ primitiveSamReader = new CRAMFileReader(
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+ IOUtil.maybeBufferedSeekableStream(data.asUnbufferedSeekableStream()),
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+ bufferedIndexStream, referenceSource, validationStringency);
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+ } else {
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+ // assume its a SAM file/no index
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+ LOG.warn("Unable to detect file format from input URL or stream, assuming SAM format.");
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+ primitiveSamReader = new SAMTextReader(
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+ IOUtil.toBufferedStream(data.asUnbufferedInputStream()),
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+ validationStringency, this.samRecordFactory);
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+ }
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+ } else if (type == InputResource.Type.SRA_ACCESSION) {
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+ primitiveSamReader = new SRAFileReader(data.asSRAAccession());
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+ } else {
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+ InputStream bufferedStream =
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+ IOUtil.maybeBufferInputStream(
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+ data.asUnbufferedInputStream(),
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+ Math.max(Defaults.BUFFER_SIZE, BlockCompressedStreamConstants.MAX_COMPRESSED_BLOCK_SIZE)
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+ );
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+ File sourceFile = data.asFile();
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+ // calling asFile is safe even if indexMaybe is a Google Cloud Storage bucket
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+ // (in that case we just get null)
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+ final File indexFile = indexMaybe == null ? null : indexMaybe.asFile();
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+ if (SamStreams.isBAMFile(bufferedStream)) {
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+ if (sourceFile == null || !sourceFile.isFile()) {
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+ // check whether we can seek
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+ final SeekableStream indexSeekable = indexMaybe == null ? null : indexMaybe.asUnbufferedSeekableStream();
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+ // do not close bufferedStream, it's the same stream we're getting here.
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+ SeekableStream sourceSeekable = data.asUnbufferedSeekableStream();
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+ if (null == sourceSeekable || null == indexSeekable) {
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+ // not seekable.
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+ // it's OK that we consumed a bit of the stream already, this ctor expects it.
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+ primitiveSamReader = new BAMFileReader(bufferedStream, indexFile, false, asynchronousIO,
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validationStringency, this.samRecordFactory, this.inflaterFactory);
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- }
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- } else if (BlockCompressedInputStream.isValidFile(bufferedStream)) {
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- primitiveSamReader = new SAMTextReader(new BlockCompressedInputStream(bufferedStream), validationStringency, this.samRecordFactory);
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- } else if (SamStreams.isGzippedSAMFile(bufferedStream)) {
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- primitiveSamReader = new SAMTextReader(new GZIPInputStream(bufferedStream), validationStringency, this.samRecordFactory);
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- } else if (SamStreams.isCRAMFile(bufferedStream)) {
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- if (referenceSource == null) {
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- referenceSource = ReferenceSource.getDefaultCRAMReferenceSource();
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- }
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- if (sourceFile == null || !sourceFile.isFile()) {
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- primitiveSamReader = new CRAMFileReader(bufferedStream, indexFile, referenceSource, validationStringency);
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} else {
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- bufferedStream.close();
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- primitiveSamReader = new CRAMFileReader(sourceFile, indexFile, referenceSource, validationStringency);
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- }
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- } else if (sourceFile != null && isSra(sourceFile)) {
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- if (bufferedStream != null) {
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- bufferedStream.close();
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+ // seekable.
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+ // need to return to the beginning because it's the same stream we used earlier
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+ // and read a bit from, and that form of the ctor expects the stream to start at 0.
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+ sourceSeekable.seek(0);
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+ primitiveSamReader = new BAMFileReader(
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+ sourceSeekable, indexSeekable, false, asynchronousIO, validationStringency,
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+ this.samRecordFactory, this.inflaterFactory);
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}
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- primitiveSamReader = new SRAFileReader(new SRAAccession(sourceFile.getPath()));
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} else {
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- if (indexDefined) {
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- bufferedStream.close();
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- throw new RuntimeException("Cannot use index file with textual SAM file");
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- }
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- primitiveSamReader = new SAMTextReader(bufferedStream, sourceFile, validationStringency, this.samRecordFactory);
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+ bufferedStream.close();
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+ primitiveSamReader = new BAMFileReader(
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+ sourceFile, indexFile, false, asynchronousIO,
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+ validationStringency, this.samRecordFactory, this.inflaterFactory);
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+ }
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+ } else if (BlockCompressedInputStream.isValidFile(bufferedStream)) {
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+ primitiveSamReader = new SAMTextReader(new BlockCompressedInputStream(bufferedStream), validationStringency, this.samRecordFactory);
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+ } else if (SamStreams.isGzippedSAMFile(bufferedStream)) {
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+ primitiveSamReader = new SAMTextReader(new GZIPInputStream(bufferedStream), validationStringency, this.samRecordFactory);
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+ } else if (SamStreams.isCRAMFile(bufferedStream)) {
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+ if (referenceSource == null) {
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+ referenceSource = ReferenceSource.getDefaultCRAMReferenceSource();
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+ }
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+ if (sourceFile == null || !sourceFile.isFile()) {
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+ primitiveSamReader = new CRAMFileReader(bufferedStream, indexFile, referenceSource, validationStringency);
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+ } else {
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+ bufferedStream.close();
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+ primitiveSamReader = new CRAMFileReader(sourceFile, indexFile, referenceSource, validationStringency);
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+ }
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+ } else if (sourceFile != null && isSra(sourceFile)) {
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+ if (bufferedStream != null) {
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+ bufferedStream.close();
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+ }
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+ primitiveSamReader = new SRAFileReader(new SRAAccession(sourceFile.getPath()));
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+ } else {
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+ if (indexDefined) {
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+ bufferedStream.close();
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+ throw new RuntimeException("Cannot use index file with textual SAM file");
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}
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- break;
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- default: throw new SAMException("Opening SamReader for " + type + " is not supported");
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+ primitiveSamReader = new SAMTextReader(bufferedStream, sourceFile, validationStringency, this.samRecordFactory);
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+ }
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}
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// Apply the options defined by this factory to this reader
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