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Revert "The existing code was throwing a NPE when using a CRAMFileRea…
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…der for … (#879)" (#885)

This reverts commit 9bef3fc.
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Yossi Farjoun authored May 31, 2017
1 parent 9bef3fc commit 630aa48
Showing 1 changed file with 93 additions and 98 deletions.
191 changes: 93 additions & 98 deletions src/main/java/htsjdk/samtools/SamReaderFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -303,111 +303,106 @@ public SamReader open(final SamInputResource resource) {
return reader;
}
}
switch (type) {
case PATH: case SEEKABLE_STREAM: case URL:
if (SamStreams.sourceLikeBam(data.asUnbufferedSeekableStream())) {
final SeekableStream bufferedIndexStream;
if (indexDefined && indexMaybe.asUnbufferedSeekableStream() != null) {
bufferedIndexStream = IOUtil.maybeBufferedSeekableStream(indexMaybe.asUnbufferedSeekableStream());
} else {
// TODO: Throw an exception here? An index _may_ have been provided, but we're ignoring it
bufferedIndexStream = null;
}

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

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

// Apply the options defined by this factory to this reader
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