Bundle referenceBundleFromFastaPath(
+ final IOPath fastaPath, final Function ioPathConstructor) {
final BundleBuilder referenceBundleBuilder = new BundleBuilder();
referenceBundleBuilder.addPrimary(new IOPathResource(fastaPath, BundleResourceType.CT_HAPLOID_REFERENCE));
final Path dictPath = ReferenceSequenceFileFactory.getDefaultDictionaryForReferenceSequence(fastaPath.toPath());
if (Files.exists(dictPath)) {
- referenceBundleBuilder.addSecondary(
- new IOPathResource(
- ioPathConstructor.apply(dictPath.toUri().toString()),
- BundleResourceType.CT_REFERENCE_DICTIONARY));
+ referenceBundleBuilder.addSecondary(new IOPathResource(
+ ioPathConstructor.apply(dictPath.toUri().toString()), BundleResourceType.CT_REFERENCE_DICTIONARY));
}
final Path idxPath = ReferenceSequenceFileFactory.getFastaIndexFileName(fastaPath.toPath());
if (Files.exists(idxPath)) {
- referenceBundleBuilder.addSecondary(
- new IOPathResource(
- ioPathConstructor.apply(idxPath.toUri().toString()),
- BundleResourceType.CT_REFERENCE_INDEX));
+ referenceBundleBuilder.addSecondary(new IOPathResource(
+ ioPathConstructor.apply(idxPath.toUri().toString()), BundleResourceType.CT_REFERENCE_INDEX));
}
try {
if (IOUtil.isBlockCompressed(fastaPath.toPath(), true)) {
final Path gziPath = GZIIndex.resolveIndexNameForBgzipFile(fastaPath.toPath());
- referenceBundleBuilder.addSecondary(
- new IOPathResource(
- ioPathConstructor.apply(gziPath.toUri().toString()),
- BundleResourceType.CT_REFERENCE_INDEX_GZI));
+ referenceBundleBuilder.addSecondary(new IOPathResource(
+ ioPathConstructor.apply(gziPath.toUri().toString()),
+ BundleResourceType.CT_REFERENCE_INDEX_GZI));
}
} catch (IOException e) {
throw new HtsjdkException("Error while checking for block compression", e);
}
return referenceBundleBuilder.build();
}
-
}
diff --git a/src/main/java/htsjdk/beta/plugin/registry/HtsCodecRegistry.java b/src/main/java/htsjdk/beta/plugin/registry/HtsCodecRegistry.java
index 9ee13a3c68..ad226c9f17 100644
--- a/src/main/java/htsjdk/beta/plugin/registry/HtsCodecRegistry.java
+++ b/src/main/java/htsjdk/beta/plugin/registry/HtsCodecRegistry.java
@@ -1,11 +1,12 @@
package htsjdk.beta.plugin.registry;
+import htsjdk.beta.exception.HtsjdkPluginException;
+import htsjdk.beta.exception.HtsjdkUnsupportedOperationException;
import htsjdk.beta.plugin.HtsCodec;
import htsjdk.beta.plugin.hapref.HaploidReferenceCodec;
import htsjdk.beta.plugin.reads.ReadsCodec;
import htsjdk.beta.plugin.variants.VariantsCodec;
-import htsjdk.beta.exception.HtsjdkPluginException;
-import htsjdk.beta.exception.HtsjdkUnsupportedOperationException;
+
/**
* A registry for tracking {@link HtsCodec} instances.
*
@@ -26,7 +27,7 @@ public class HtsCodecRegistry {
* Create a registry. Protected to prevent use outside of the registry package. To create
* a private registry from outside the registry package, use {@link #createPrivateRegistry}.
*/
- protected HtsCodecRegistry() { }
+ protected HtsCodecRegistry() {}
/**
* Add a codec to the registry. If a codec that supports the same (format, version) (determined
@@ -66,15 +67,21 @@ protected HtsCodecRegistry() { }
*
* @return a mutable registry instance for private use
*/
- public synchronized static HtsCodecRegistry createPrivateRegistry() {
+ public static synchronized HtsCodecRegistry createPrivateRegistry() {
final HtsCodecRegistry privateRegistry = new HtsCodecRegistry();
// propagate the codecs from the sourceRegistry to the new registry
- HtsDefaultRegistry.htsDefaultCodecRegistry.getHaploidReferenceResolver().getCodecs()
+ HtsDefaultRegistry.htsDefaultCodecRegistry
+ .getHaploidReferenceResolver()
+ .getCodecs()
+ .forEach(c -> privateRegistry.registerCodec(c));
+ HtsDefaultRegistry.htsDefaultCodecRegistry
+ .getReadsResolver()
+ .getCodecs()
.forEach(c -> privateRegistry.registerCodec(c));
- HtsDefaultRegistry.htsDefaultCodecRegistry.getReadsResolver().getCodecs().
- forEach(c -> privateRegistry.registerCodec(c));
- HtsDefaultRegistry.htsDefaultCodecRegistry.getVariantsResolver().getCodecs()
+ HtsDefaultRegistry.htsDefaultCodecRegistry
+ .getVariantsResolver()
+ .getCodecs()
.forEach(c -> privateRegistry.registerCodec(c));
return privateRegistry;
}
@@ -84,21 +91,25 @@ public synchronized static HtsCodecRegistry createPrivateRegistry() {
*
* @return the {@link HaploidReferenceResolver} for this registry
*/
- public synchronized HaploidReferenceResolver getHaploidReferenceResolver() { return htsHaploidReferenceResolver; }
+ public synchronized HaploidReferenceResolver getHaploidReferenceResolver() {
+ return htsHaploidReferenceResolver;
+ }
/**
* Get the {@link ReadsResolver} for this registry.
*
* @return the {@link ReadsResolver} for this registry
*/
- public synchronized ReadsResolver getReadsResolver() { return htsReadsResolver; }
+ public synchronized ReadsResolver getReadsResolver() {
+ return htsReadsResolver;
+ }
/**
* Get the {@link VariantsResolver} for this registry.
*
* @return the {@link VariantsResolver} for this registry
*/
- public synchronized VariantsResolver getVariantsResolver() { return htsVariantsResolver; }
-
+ public synchronized VariantsResolver getVariantsResolver() {
+ return htsVariantsResolver;
+ }
}
-
diff --git a/src/main/java/htsjdk/beta/plugin/registry/HtsCodecResolver.java b/src/main/java/htsjdk/beta/plugin/registry/HtsCodecResolver.java
index dbfc7d7ed2..cd83db6b4e 100644
--- a/src/main/java/htsjdk/beta/plugin/registry/HtsCodecResolver.java
+++ b/src/main/java/htsjdk/beta/plugin/registry/HtsCodecResolver.java
@@ -1,18 +1,17 @@
package htsjdk.beta.plugin.registry;
+import htsjdk.annotations.InternalAPI;
+import htsjdk.beta.exception.HtsjdkException;
import htsjdk.beta.exception.HtsjdkIOException;
-import htsjdk.beta.plugin.HtsCodec;
-import htsjdk.beta.plugin.HtsVersion;
+import htsjdk.beta.exception.HtsjdkPluginException;
import htsjdk.beta.io.bundle.Bundle;
import htsjdk.beta.io.bundle.BundleResource;
import htsjdk.beta.io.bundle.SignatureStream;
-import htsjdk.beta.exception.HtsjdkException;
-import htsjdk.beta.exception.HtsjdkPluginException;
+import htsjdk.beta.plugin.HtsCodec;
+import htsjdk.beta.plugin.HtsVersion;
import htsjdk.io.IOPath;
import htsjdk.samtools.util.Log;
-import htsjdk.annotations.InternalAPI;
import htsjdk.utils.ValidationUtils;
-
import java.io.IOException;
import java.util.Collections;
import java.util.HashMap;
@@ -37,8 +36,8 @@
public class HtsCodecResolver> {
private static final Log LOG = Log.getInstance(HtsCodecResolver.class);
- final static String NO_SUPPORTING_CODEC_ERROR = "No registered codec accepts the provided resource";
- final static String MULTIPLE_SUPPORTING_CODECS_ERROR = "Multiple codecs accept the provided resource";
+ static final String NO_SUPPORTING_CODEC_ERROR = "No registered codec accepts the provided resource";
+ static final String MULTIPLE_SUPPORTING_CODECS_ERROR = "Multiple codecs accept the provided resource";
private final String requiredContentType;
private final Map> codecs = new HashMap<>();
@@ -75,9 +74,9 @@ public C registerCodec(final C codec) {
// update the version map for this codec
final C oldCodec = versionMap.put(codec.getVersion(), codec);
if (oldCodec != null) {
- LOG.warn(String.format("A previously registered HTS codec (%s) was replaced with the (%s) codec ",
- oldCodec.getDisplayName(),
- codec.getDisplayName()));
+ LOG.warn(String.format(
+ "A previously registered HTS codec (%s) was replaced with the (%s) codec ",
+ oldCodec.getDisplayName(), codec.getDisplayName()));
}
return oldCodec;
}
@@ -149,15 +148,14 @@ public C resolveForDecoding(final Bundle bundle) {
final Optional optFormatString = bundleResource.getFileFormat();
final List candidateCodecs = resolveForFormat(optFormatString);
- final List resolvedCodecs = bundleResource.getIOPath().isPresent() ?
- resolveForDecodingIOPath(bundleResource, candidateCodecs) :
- resolveForDecodingStream(bundleResource, candidateCodecs);
+ final List resolvedCodecs = bundleResource.getIOPath().isPresent()
+ ? resolveForDecodingIOPath(bundleResource, candidateCodecs)
+ : resolveForDecodingStream(bundleResource, candidateCodecs);
return getOneOrThrow(
resolvedCodecs,
- () -> String.format("%s/%s",
- optFormatString.isPresent () ? optFormatString.get() : "(NONE)",
- bundleResource));
+ () -> String.format(
+ "%s/%s", optFormatString.isPresent() ? optFormatString.get() : "(NONE)", bundleResource));
}
/**
@@ -180,7 +178,9 @@ public C resolveForDecoding(final Bundle bundle) {
* @throws HtsjdkPluginException if more than one codec claims to handle the resource. this usually indicates
* that the registry contains an incorrectly written codec.
*/
- public C resolveForEncoding(final Bundle bundle) { return resolveForEncoding(bundle, HtsVersion.NEWEST_VERSION); }
+ public C resolveForEncoding(final Bundle bundle) {
+ return resolveForEncoding(bundle, HtsVersion.NEWEST_VERSION);
+ }
/**
* Inspect a bundle and find a codec that can encode to the primary resource using the format version
@@ -208,16 +208,15 @@ public C resolveForEncoding(final Bundle bundle, final HtsVersion htsVersion) {
final List candidateCodecs = resolveForFormat(optFormatString);
final Optional ioPath = bundleResource.getIOPath();
- final List filteredCodecs = bundleResource.getIOPath().isPresent() ?
- resolveForEncodingIOPath(ioPath.get(), candidateCodecs) :
- candidateCodecs; // there isn't anything else to probe when the output is to a stream
+ final List filteredCodecs = bundleResource.getIOPath().isPresent()
+ ? resolveForEncodingIOPath(ioPath.get(), candidateCodecs)
+ : candidateCodecs; // there isn't anything else to probe when the output is to a stream
final List resolvedCodecs = filterByVersion(filteredCodecs, htsVersion);
return getOneOrThrow(
resolvedCodecs,
- () -> String.format("%s/%s",
- optFormatString.isPresent () ? optFormatString.get() : "(NONE)",
- bundleResource));
+ () -> String.format(
+ "%s/%s", optFormatString.isPresent() ? optFormatString.get() : "(NONE)", bundleResource));
}
/**
@@ -245,9 +244,9 @@ public List resolveForFormat(final String format) {
* @throws HtsjdkException if no registered codecs can handle the resource
*/
public C resolveFormatAndVersion(final String format, final HtsVersion formatVersion) {
- final List matchingCodecs = resolveForFormat(format)
- .stream()
- .filter(codec -> codec.getFileFormat().equals(format) && codec.getVersion().equals(formatVersion))
+ final List matchingCodecs = resolveForFormat(format).stream()
+ .filter(codec -> codec.getFileFormat().equals(format)
+ && codec.getVersion().equals(formatVersion))
.collect(Collectors.toList());
return getOneOrThrow(matchingCodecs, () -> String.format("%s/%s", format, formatVersion));
}
@@ -259,11 +258,8 @@ public C resolveFormatAndVersion(final String format, final HtsVersion formatVer
*/
public List getCodecs() {
// flatten out the codecs into a single list
- final List codecList = codecs
- .values()
- .stream()
- .flatMap(map -> map.values().stream())
- .collect(Collectors.toList());
+ final List codecList =
+ codecs.values().stream().flatMap(map -> map.values().stream()).collect(Collectors.toList());
return codecList;
}
@@ -296,35 +292,28 @@ private List resolveForDecodingStream(final BundleResource bundleResource, fi
final byte[] signatureBuffer = getSignatureProbeBuffer(bundleResource, candidateCodecs);
return candidateCodecs.stream()
.filter(codec -> codec.canDecodeSignature(
- new SignatureStream(signatureBuffer.length, signatureBuffer),
- bundleResource.getDisplayName()))
+ new SignatureStream(signatureBuffer.length, signatureBuffer), bundleResource.getDisplayName()))
.collect(Collectors.toList());
}
- private final byte[] getSignatureProbeBuffer(
- final BundleResource bundleResource,
- final List candidateCodecs) {
+ private final byte[] getSignatureProbeBuffer(final BundleResource bundleResource, final List candidateCodecs) {
final int maxSignatureProbeLength = getMaxSignatureProbeLength(candidateCodecs);
- try (final SignatureStream probingStream =
- bundleResource.getIOPath().isPresent() ?
- getIOPathSignatureProbingStream(bundleResource, maxSignatureProbeLength) :
- bundleResource.getSignatureStream(maxSignatureProbeLength)) {
+ try (final SignatureStream probingStream = bundleResource.getIOPath().isPresent()
+ ? getIOPathSignatureProbingStream(bundleResource, maxSignatureProbeLength)
+ : bundleResource.getSignatureStream(maxSignatureProbeLength)) {
// we need to recreate a stream over the underlying signature for each codec,
// since some implementations may use their own mark/reset pairs
final byte[] signatureBytes = new byte[probingStream.getSignaturePrefixLength()];
final int readSize = probingStream.read(signatureBytes);
if (readSize != maxSignatureProbeLength) {
- throw new HtsjdkPluginException(
- String.format("Failure to read %d bytes from signature stream for %s (only read %d)",
- maxSignatureProbeLength,
- bundleResource,
- readSize));
+ throw new HtsjdkPluginException(String.format(
+ "Failure to read %d bytes from signature stream for %s (only read %d)",
+ maxSignatureProbeLength, bundleResource, readSize));
}
return signatureBytes;
} catch (IOException e) {
throw new HtsjdkIOException(
- String.format("error closing signature stream for %s", bundleResource.getDisplayName()),
- e);
+ String.format("error closing signature stream for %s", bundleResource.getDisplayName()), e);
}
}
@@ -339,21 +328,19 @@ private List resolveForEncodingIOPath(final IOPath ioPath, final List cand
final List filteredCodecs = uriHandlers.isEmpty() ? candidateCodecs : uriHandlers;
// reduce our candidates based on uri and IOPath
- return filteredCodecs.stream()
- .filter(c -> c.canDecodeURI(ioPath))
- .collect(Collectors.toList());
+ return filteredCodecs.stream().filter(c -> c.canDecodeURI(ioPath)).collect(Collectors.toList());
}
private int getMaxSignatureProbeLength(final List candidateCodecs) {
// find the longest signature probe length of any candidate
return candidateCodecs.stream()
.map(codec -> codec.getSignatureProbeLength())
- .max(Integer::compare).orElse(0);
+ .max(Integer::compare)
+ .orElse(0);
}
private SignatureStream getIOPathSignatureProbingStream(
- final BundleResource bundleResource,
- final int streamPrefixSize) {
+ final BundleResource bundleResource, final int streamPrefixSize) {
ValidationUtils.validateArg(bundleResource.getIOPath().isPresent(), "an IOPath resource is required");
final IOPath inputPath = bundleResource.getIOPath().get();
if (!inputPath.hasFileSystemProvider()) {
@@ -364,11 +351,10 @@ private SignatureStream getIOPathSignatureProbingStream(
// "claimURI" implementations, or else it would be a known protocol such as "gs://" for
// which the user expected a file system to be present. It likely represents user error
// (a user entered "hdf://" instead of "hdfs://"), and it will fail anyway, so throw.
- throw new IllegalArgumentException(
- String.format("The resource (%s) specifies a custom protocol (%s) " +
- "which no registered codec claims, and for which no NIO file system provider is available",
- bundleResource,
- inputPath.getURI().getScheme()));
+ throw new IllegalArgumentException(String.format(
+ "The resource (%s) specifies a custom protocol (%s) "
+ + "which no registered codec claims, and for which no NIO file system provider is available",
+ bundleResource, inputPath.getURI().getScheme()));
}
return bundleResource.getSignatureStream(streamPrefixSize);
}
@@ -387,10 +373,12 @@ protected List filterByVersion(final List candidateCodecs, final HtsVersio
// version (since there still can be more than one)
final HtsVersion newestVersion = candidateCodecs.stream()
.map(c -> c.getVersion())
- .reduce(candidateCodecs.get(0).getVersion(),
+ .reduce(
+ candidateCodecs.get(0).getVersion(),
(HtsVersion a, HtsVersion b) -> a.compareTo(b) > 0 ? a : b);
- return candidateCodecs.stream().filter(
- c -> c.getVersion().equals(newestVersion)).collect(Collectors.toList());
+ return candidateCodecs.stream()
+ .filter(c -> c.getVersion().equals(newestVersion))
+ .collect(Collectors.toList());
} else {
return candidateCodecs.stream()
.filter(c -> c.getVersion().equals(htsVersion))
@@ -402,17 +390,13 @@ protected List filterByVersion(final List candidateCodecs, final HtsVersio
// or otherwise all registered codecs for this codec format.
private List resolveForFormat(final Optional optFormatString) {
final List candidateCodecs =
- optFormatString.isPresent() ?
- resolveForFormat(optFormatString.get()) :
- getCodecs();
+ optFormatString.isPresent() ? resolveForFormat(optFormatString.get()) : getCodecs();
if (optFormatString.isPresent() && candidateCodecs.isEmpty()) {
// warn if the resource format string is present, but doesn't map to any codec registered
// with this resolver (/content type).
LOG.warn(String.format(
"The specified format string (%s) does not correspond to any registered codec for content type (%s)",
- optFormatString.get(),
- requiredContentType));
-
+ optFormatString.get(), requiredContentType));
}
return candidateCodecs;
}
@@ -426,14 +410,13 @@ private List getURIOwners(final List candidateCodecs, final IOPath ioPath)
if (isCustomURI) {
// ensure that all codecs that claim to own this URI honor the contract that says if canDecodeURI
// returns true, ownsURI must also return true for the same IOPath
- uriHandlers.stream().forEach(
- codec -> {
- if (!codec.canDecodeURI(ioPath)) {
- throw new HtsjdkPluginException(
- String.format("The %s codec returned true for ownsURI but false for canDecodeURI for path: %s",
- codec,
- ioPath.getURI()));
- }});
+ uriHandlers.stream().forEach(codec -> {
+ if (!codec.canDecodeURI(ioPath)) {
+ throw new HtsjdkPluginException(String.format(
+ "The %s codec returned true for ownsURI but false for canDecodeURI for path: %s",
+ codec, ioPath.getURI()));
+ }
+ });
}
return uriHandlers;
}
@@ -446,21 +429,18 @@ private final BundleResource getPrimaryResource(final Bundle bundle, final boole
if (!requiredContentType.equals(bundlePrimaryContentType)) {
throw new IllegalArgumentException(String.format(
"The primary content type (%s) for the resource does not match the requested content type (%s).",
- bundlePrimaryContentType,
- requiredContentType));
+ bundlePrimaryContentType, requiredContentType));
}
// Make sure the resource type is appropriate for encoding or decoding, as requested by the caller
if (forEncoding && !bundleResource.hasInputType()) {
- throw new IllegalArgumentException(
- String.format("The %s resource found (%s) cannot be used as an input resource",
- requiredContentType,
- bundleResource));
+ throw new IllegalArgumentException(String.format(
+ "The %s resource found (%s) cannot be used as an input resource",
+ requiredContentType, bundleResource));
} else if (!forEncoding && !bundleResource.hasOutputType()) { // for decoding
- throw new IllegalArgumentException(
- String.format("The %s resource found (%s) cannot be used as an output resource",
- requiredContentType,
- bundleResource));
+ throw new IllegalArgumentException(String.format(
+ "The %s resource found (%s) cannot be used as an output resource",
+ requiredContentType, bundleResource));
}
return bundleResource;
@@ -468,13 +448,9 @@ private final BundleResource getPrimaryResource(final Bundle bundle, final boole
@InternalAPI
static > C getOneOrThrow(
- final List resolvedCodecs,
- final Supplier contextMessage) {
+ final List resolvedCodecs, final Supplier contextMessage) {
if (resolvedCodecs.size() == 0) {
- throw new HtsjdkException(String.format(
- "%s %s",
- NO_SUPPORTING_CODEC_ERROR,
- contextMessage.get()));
+ throw new HtsjdkException(String.format("%s %s", NO_SUPPORTING_CODEC_ERROR, contextMessage.get()));
} else if (resolvedCodecs.size() > 1) {
final String multipleCodecsMessage = String.format(
"%s (%s)\n%s\nThis indicates an internal error in one or more of the codecs:",
@@ -486,5 +462,4 @@ private final BundleResource getPrimaryResource(final Bundle bundle, final boole
return resolvedCodecs.get(0);
}
}
-
}
diff --git a/src/main/java/htsjdk/beta/plugin/registry/HtsDefaultRegistry.java b/src/main/java/htsjdk/beta/plugin/registry/HtsDefaultRegistry.java
index 6a14758668..a241221399 100644
--- a/src/main/java/htsjdk/beta/plugin/registry/HtsDefaultRegistry.java
+++ b/src/main/java/htsjdk/beta/plugin/registry/HtsDefaultRegistry.java
@@ -17,7 +17,9 @@ public class HtsDefaultRegistry {
/**
* statically populate the default registry with any codecs on the classpath
*/
- static {ServiceLoader.load(HtsCodec.class).forEach(htsDefaultCodecRegistry::registerCodec);}
+ static {
+ ServiceLoader.load(HtsCodec.class).forEach(htsDefaultCodecRegistry::registerCodec);
+ }
/**
* Grt the {@link HaploidReferenceResolver} resolver for this registry.
@@ -25,7 +27,8 @@ public class HtsDefaultRegistry {
* @return the {@link HaploidReferenceResolver} resolver for this registry
*/
public static synchronized HaploidReferenceResolver getHaploidReferenceResolver() {
- return htsDefaultCodecRegistry.getHaploidReferenceResolver(); }
+ return htsDefaultCodecRegistry.getHaploidReferenceResolver();
+ }
/**
* Gt the {@link ReadsResolver} resolver for this registry.
@@ -33,7 +36,8 @@ public static synchronized HaploidReferenceResolver getHaploidReferenceResolver(
* @return the {@link ReadsResolver} resolver for this registry
*/
public static synchronized ReadsResolver getReadsResolver() {
- return htsDefaultCodecRegistry.getReadsResolver(); }
+ return htsDefaultCodecRegistry.getReadsResolver();
+ }
/**
* Get the {@link VariantsResolver} resolver for this registry.
@@ -41,6 +45,6 @@ public static synchronized ReadsResolver getReadsResolver() {
* @return the {@link VariantsResolver} resolver for this registry
*/
public static synchronized VariantsResolver getVariantsResolver() {
- return htsDefaultCodecRegistry.getVariantsResolver(); }
-
+ return htsDefaultCodecRegistry.getVariantsResolver();
+ }
}
diff --git a/src/main/java/htsjdk/beta/plugin/registry/ReadsResolver.java b/src/main/java/htsjdk/beta/plugin/registry/ReadsResolver.java
index b89ffc4a10..90fb0796c2 100644
--- a/src/main/java/htsjdk/beta/plugin/registry/ReadsResolver.java
+++ b/src/main/java/htsjdk/beta/plugin/registry/ReadsResolver.java
@@ -2,9 +2,9 @@
import htsjdk.beta.exception.HtsjdkException;
import htsjdk.beta.exception.HtsjdkPluginException;
-import htsjdk.beta.plugin.HtsVersion;
import htsjdk.beta.io.bundle.Bundle;
import htsjdk.beta.io.bundle.BundleResourceType;
+import htsjdk.beta.plugin.HtsVersion;
import htsjdk.beta.plugin.reads.ReadsBundle;
import htsjdk.beta.plugin.reads.ReadsCodec;
import htsjdk.beta.plugin.reads.ReadsDecoder;
@@ -25,7 +25,7 @@
* {@link ReadsCodec}s, such as {@link ReadsDecoder}, {@link ReadsEncoder},
* {@link htsjdk.beta.plugin.reads.ReadsDecoderOptions}.
*/
-public class ReadsResolver extends HtsCodecResolver{
+public class ReadsResolver extends HtsCodecResolver {
/**
* Create a ReadsResolver.
@@ -64,9 +64,7 @@ public ReadsDecoder getReadsDecoder(final IOPath inputPath) {
* @throws HtsjdkPluginException if more than one codec claims to handle the resource. this usually indicates
* that the registry contains an incorrectly written codec.
*/
- public ReadsDecoder getReadsDecoder(
- final IOPath inputPath,
- final ReadsDecoderOptions readsDecoderOptions) {
+ public ReadsDecoder getReadsDecoder(final IOPath inputPath, final ReadsDecoderOptions readsDecoderOptions) {
ValidationUtils.nonNull(inputPath, "Input path");
ValidationUtils.nonNull(readsDecoderOptions, "Decoder options");
@@ -102,9 +100,7 @@ public ReadsDecoder getReadsDecoder(final Bundle inputBundle) {
* that the registry contains an incorrectly written codec.
*/
@SuppressWarnings("unchecked")
- public ReadsDecoder getReadsDecoder(
- final Bundle inputBundle,
- final ReadsDecoderOptions readsDecoderOptions) {
+ public ReadsDecoder getReadsDecoder(final Bundle inputBundle, final ReadsDecoderOptions readsDecoderOptions) {
ValidationUtils.nonNull(inputBundle, "Input bundle");
ValidationUtils.nonNull(readsDecoderOptions, "Decoder options");
@@ -143,9 +139,7 @@ public ReadsEncoder getReadsEncoder(final IOPath outputPath) {
* @throws HtsjdkPluginException if more than one codec claims to handle the resource. this usually indicates
* that the registry contains an incorrectly written codec.
*/
- public ReadsEncoder getReadsEncoder(
- final IOPath outputPath,
- final ReadsEncoderOptions readsEncoderOptions) {
+ public ReadsEncoder getReadsEncoder(final IOPath outputPath, final ReadsEncoderOptions readsEncoderOptions) {
ValidationUtils.nonNull(outputPath, "Output path");
ValidationUtils.nonNull(readsEncoderOptions, "Encoder options");
@@ -168,9 +162,7 @@ public ReadsEncoder getReadsEncoder(
* that the registry contains an incorrectly written codec.
*/
@SuppressWarnings("unchecked")
- public ReadsEncoder getReadsEncoder(
- final Bundle outputBundle,
- final ReadsEncoderOptions readsEncoderOptions) {
+ public ReadsEncoder getReadsEncoder(final Bundle outputBundle, final ReadsEncoderOptions readsEncoderOptions) {
ValidationUtils.nonNull(outputBundle, "outputBundle");
ValidationUtils.nonNull(readsEncoderOptions, "Encoder options");
@@ -200,8 +192,7 @@ public ReadsEncoder getReadsEncoder(
ValidationUtils.nonNull(readsFormat, "Reads format");
ValidationUtils.nonNull(formatVersion, "File format version");
- return (ReadsEncoder) resolveFormatAndVersion(readsFormat, formatVersion)
- .getEncoder(outputBundle, readsEncoderOptions);
+ return (ReadsEncoder)
+ resolveFormatAndVersion(readsFormat, formatVersion).getEncoder(outputBundle, readsEncoderOptions);
}
-
}
diff --git a/src/main/java/htsjdk/beta/plugin/registry/VariantsResolver.java b/src/main/java/htsjdk/beta/plugin/registry/VariantsResolver.java
index dd8841377e..e755fa219c 100644
--- a/src/main/java/htsjdk/beta/plugin/registry/VariantsResolver.java
+++ b/src/main/java/htsjdk/beta/plugin/registry/VariantsResolver.java
@@ -3,11 +3,11 @@
import htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFCodecV4_2;
import htsjdk.beta.exception.HtsjdkException;
import htsjdk.beta.exception.HtsjdkPluginException;
-import htsjdk.beta.plugin.HtsVersion;
import htsjdk.beta.io.bundle.Bundle;
import htsjdk.beta.io.bundle.BundleBuilder;
import htsjdk.beta.io.bundle.BundleResourceType;
import htsjdk.beta.io.bundle.IOPathResource;
+import htsjdk.beta.plugin.HtsVersion;
import htsjdk.beta.plugin.variants.VariantsCodec;
import htsjdk.beta.plugin.variants.VariantsDecoder;
import htsjdk.beta.plugin.variants.VariantsDecoderOptions;
@@ -62,8 +62,7 @@ public VariantsDecoder getVariantsDecoder(final IOPath inputPath) {
* that the registry contains an incorrectly written codec.
*/
public VariantsDecoder getVariantsDecoder(
- final IOPath inputPath,
- final VariantsDecoderOptions variantsDecoderOptions) {
+ final IOPath inputPath, final VariantsDecoderOptions variantsDecoderOptions) {
ValidationUtils.nonNull(inputPath, "Input path");
ValidationUtils.nonNull(variantsDecoderOptions, "Decoder options");
@@ -102,8 +101,7 @@ public VariantsDecoder getVariantsDecoder(final Bundle inputBundle) {
*/
@SuppressWarnings("unchecked")
public VariantsDecoder getVariantsDecoder(
- final Bundle inputBundle,
- final VariantsDecoderOptions variantsDecoderOptions) {
+ final Bundle inputBundle, final VariantsDecoderOptions variantsDecoderOptions) {
ValidationUtils.nonNull(inputBundle, "Input bundle");
ValidationUtils.nonNull(variantsDecoderOptions, "Decoder options");
@@ -137,8 +135,7 @@ public VariantsEncoder getVariantsEncoder(final IOPath outputPath) {
* that the registry contains an incorrectly written codec.
*/
public VariantsEncoder getVariantsEncoder(
- final IOPath outputPath,
- final VariantsEncoderOptions variantsEncoderOptions) {
+ final IOPath outputPath, final VariantsEncoderOptions variantsEncoderOptions) {
ValidationUtils.nonNull(outputPath, "Output path");
ValidationUtils.nonNull(variantsEncoderOptions, "Encoder options");
@@ -159,12 +156,11 @@ public VariantsEncoder getVariantsEncoder(
* that the registry contains an incorrectly written codec.
*/
public VariantsEncoder getVariantsEncoder(
- final Bundle outputBundle,
- final VariantsEncoderOptions variantsEncoderOptions) {
+ final Bundle outputBundle, final VariantsEncoderOptions variantsEncoderOptions) {
ValidationUtils.nonNull(outputBundle, "Output bundle");
ValidationUtils.nonNull(variantsEncoderOptions, "Encoder options");
- //NOTE: we can't allow the resolver to choose the newest registered codec when writing a
+ // NOTE: we can't allow the resolver to choose the newest registered codec when writing a
// VCF, since the newest codec is v4.3, which has no encoder, so for now explicitly select v4.2
final VariantsCodec variantsCodec = resolveForEncoding(outputBundle, VCFCodecV4_2.VCF_V42_VERSION);
return (VariantsEncoder) variantsCodec.getEncoder(outputBundle, variantsEncoderOptions);
@@ -194,8 +190,7 @@ public VariantsEncoder getVariantsEncoder(
ValidationUtils.nonNull(variantsFormat, "Format");
ValidationUtils.nonNull(formatVersion, "Format version");
- return (VariantsEncoder) resolveFormatAndVersion(variantsFormat, formatVersion)
- .getEncoder(outputBundle, variantsEncoderOptions);
+ return (VariantsEncoder)
+ resolveFormatAndVersion(variantsFormat, formatVersion).getEncoder(outputBundle, variantsEncoderOptions);
}
-
}
diff --git a/src/main/java/htsjdk/beta/plugin/variants/VariantsBundle.java b/src/main/java/htsjdk/beta/plugin/variants/VariantsBundle.java
index 2a8dae15e4..128d0d2840 100644
--- a/src/main/java/htsjdk/beta/plugin/variants/VariantsBundle.java
+++ b/src/main/java/htsjdk/beta/plugin/variants/VariantsBundle.java
@@ -8,7 +8,6 @@
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.Tuple;
import htsjdk.utils.ValidationUtils;
-
import java.io.Serial;
import java.io.Serializable;
import java.nio.file.Files;
@@ -30,6 +29,7 @@
public class VariantsBundle extends Bundle implements Serializable {
@Serial
private static final long serialVersionUID = 1L;
+
private static final Log LOG = Log.getInstance(VariantsBundle.class);
/**
@@ -108,8 +108,8 @@ public static VariantsBundle getVariantsBundleFromPath(final IOPath jsonPath) {
* @param ioPathConstructor a function that takes a string and returns an IOPath-derived class of type {@code T}
* @return a {@link VariantsBundle} created from jsonPath
*/
- public static VariantsBundle getVariantsBundleFromPath(final IOPath jsonPath,
- final Function ioPathConstructor) {
+ public static VariantsBundle getVariantsBundleFromPath(
+ final IOPath jsonPath, final Function ioPathConstructor) {
return getVariantsBundleFromString(IOPathUtils.getStringFromPath(jsonPath), ioPathConstructor);
}
@@ -133,9 +133,9 @@ public static VariantsBundle getVariantsBundleFromString(final String jsonString
* @return a newly created {@link htsjdk.beta.plugin.variants.VariantsBundle}
*/
public static VariantsBundle getVariantsBundleFromString(
- final String jsonString,
- final Function ioPathConstructor) {
- return new VariantsBundle(BundleJSON.toBundle(jsonString, ioPathConstructor).getResources());
+ final String jsonString, final Function ioPathConstructor) {
+ return new VariantsBundle(
+ BundleJSON.toBundle(jsonString, ioPathConstructor).getResources());
}
/**
@@ -166,8 +166,7 @@ public static Optional resolveIndex(final IOPath variants) {
* if it can be found
*/
public static Optional resolveIndex(
- final T variantsHtsPath,
- final Function ioPathConstructor) {
+ final T variantsHtsPath, final Function ioPathConstructor) {
final Set indexExtensions = Set.of(FileExtensions.TRIBBLE_INDEX, FileExtensions.TABIX_INDEX);
for (final String extension : indexExtensions) {
final T putativeIndexPath = IOPathUtils.appendExtension(variantsHtsPath, extension, ioPathConstructor);
@@ -185,9 +184,7 @@ private static IOPathResource toInputResource(final String pr
if (providedContentType != null && !typePair.get().a.equals(providedContentType)) {
LOG.warn(String.format(
"Provided content type \"%s\" for \"%s\" doesn't match derived content type \"%s\"",
- providedContentType,
- ioPath.getRawInputString(),
- typePair.get().a));
+ providedContentType, ioPath.getRawInputString(), typePair.get().a));
}
}
return new IOPathResource(ioPath, providedContentType);
@@ -206,9 +203,11 @@ private static Optional> getInferredCon
if (extension.isPresent()) {
final String ext = extension.get();
if (ext.equals(FileExtensions.VCF)) {
- return Optional.of(new Tuple<>(BundleResourceType.CT_VARIANT_CONTEXTS, BundleResourceType.FMT_VARIANTS_VCF));
+ return Optional.of(
+ new Tuple<>(BundleResourceType.CT_VARIANT_CONTEXTS, BundleResourceType.FMT_VARIANTS_VCF));
} else if (ext.equals(FileExtensions.COMPRESSED_VCF) || ext.equals(FileExtensions.COMPRESSED_VCF_BGZ)) {
- return Optional.of(new Tuple<>(BundleResourceType.CT_VARIANT_CONTEXTS, BundleResourceType.FMT_VARIANTS_VCF));
+ return Optional.of(
+ new Tuple<>(BundleResourceType.CT_VARIANT_CONTEXTS, BundleResourceType.FMT_VARIANTS_VCF));
}
}
return Optional.empty();
diff --git a/src/main/java/htsjdk/beta/plugin/variants/VariantsCodec.java b/src/main/java/htsjdk/beta/plugin/variants/VariantsCodec.java
index 97cc39306b..76591b3f5c 100644
--- a/src/main/java/htsjdk/beta/plugin/variants/VariantsCodec.java
+++ b/src/main/java/htsjdk/beta/plugin/variants/VariantsCodec.java
@@ -9,6 +9,7 @@
public interface VariantsCodec extends HtsCodec {
@Override
- default HtsContentType getContentType() { return HtsContentType.VARIANT_CONTEXTS; }
-
+ default HtsContentType getContentType() {
+ return HtsContentType.VARIANT_CONTEXTS;
+ }
}
diff --git a/src/main/java/htsjdk/beta/plugin/variants/VariantsDecoder.java b/src/main/java/htsjdk/beta/plugin/variants/VariantsDecoder.java
index 1d19461c1c..420388fcdb 100644
--- a/src/main/java/htsjdk/beta/plugin/variants/VariantsDecoder.java
+++ b/src/main/java/htsjdk/beta/plugin/variants/VariantsDecoder.java
@@ -8,4 +8,4 @@
/**
* Base class for all {@link HtsContentType#VARIANT_CONTEXTS} decoders.
*/
-public interface VariantsDecoder extends HtsDecoder { }
+public interface VariantsDecoder extends HtsDecoder {}
diff --git a/src/main/java/htsjdk/beta/plugin/variants/VariantsDecoderOptions.java b/src/main/java/htsjdk/beta/plugin/variants/VariantsDecoderOptions.java
index 46a2abad5a..9a112c2dff 100644
--- a/src/main/java/htsjdk/beta/plugin/variants/VariantsDecoderOptions.java
+++ b/src/main/java/htsjdk/beta/plugin/variants/VariantsDecoderOptions.java
@@ -1,14 +1,13 @@
package htsjdk.beta.plugin.variants;
-import htsjdk.beta.plugin.HtsDecoderOptions;
import htsjdk.annotations.InternalAPI;
-
+import htsjdk.beta.plugin.HtsDecoderOptions;
import java.nio.channels.SeekableByteChannel;
import java.util.Optional;
import java.util.function.Function;
public class VariantsDecoderOptions implements HtsDecoderOptions {
- //TODO: replace these with a prefetch size args, and use a local channel wrapper implementation
+ // TODO: replace these with a prefetch size args, and use a local channel wrapper implementation
private Function variantsChannelTransformer;
private Function indexChannelTransformer;
@@ -63,5 +62,4 @@ public VariantsDecoderOptions setIndexChannelTransformer(
this.indexChannelTransformer = indexChannelTransformer;
return this;
}
-
}
diff --git a/src/main/java/htsjdk/beta/plugin/variants/VariantsEncoder.java b/src/main/java/htsjdk/beta/plugin/variants/VariantsEncoder.java
index 9840047e69..932f3deea2 100644
--- a/src/main/java/htsjdk/beta/plugin/variants/VariantsEncoder.java
+++ b/src/main/java/htsjdk/beta/plugin/variants/VariantsEncoder.java
@@ -8,4 +8,4 @@
/**
* Base class for all {@link HtsContentType#VARIANT_CONTEXTS} encoders.
*/
-public interface VariantsEncoder extends HtsEncoder { }
+public interface VariantsEncoder extends HtsEncoder {}
diff --git a/src/main/java/htsjdk/beta/plugin/variants/VariantsEncoderOptions.java b/src/main/java/htsjdk/beta/plugin/variants/VariantsEncoderOptions.java
index 94182dc4d3..0b09fd3335 100644
--- a/src/main/java/htsjdk/beta/plugin/variants/VariantsEncoderOptions.java
+++ b/src/main/java/htsjdk/beta/plugin/variants/VariantsEncoderOptions.java
@@ -6,12 +6,11 @@
import htsjdk.samtools.Defaults;
public class VariantsEncoderOptions implements HtsEncoderOptions {
- private boolean writeSitesOnly = false;
- private boolean writeFullFormatField = false;
- private boolean allowFieldsMissingFromHeader = false;
- private boolean isAsyncIO = false;
- private int bufferSize = Defaults.NON_ZERO_BUFFER_SIZE; // 128k
-
+ private boolean writeSitesOnly = false;
+ private boolean writeFullFormatField = false;
+ private boolean allowFieldsMissingFromHeader = false;
+ private boolean isAsyncIO = false;
+ private int bufferSize = Defaults.NON_ZERO_BUFFER_SIZE; // 128k
/**
* Get the buffer size used when writing to an {@link IOPathResource}. Defaults
@@ -115,5 +114,4 @@ public VariantsEncoderOptions setWriteFullFormatField(boolean writeFullFormatFie
this.writeFullFormatField = writeFullFormatField;
return this;
}
-
}
diff --git a/src/main/java/htsjdk/io/AsyncWriterPool.java b/src/main/java/htsjdk/io/AsyncWriterPool.java
index f95bcbc7db..dab043ce39 100644
--- a/src/main/java/htsjdk/io/AsyncWriterPool.java
+++ b/src/main/java/htsjdk/io/AsyncWriterPool.java
@@ -1,7 +1,6 @@
package htsjdk.io;
import htsjdk.samtools.util.RuntimeIOException;
-
import java.io.Closeable;
import java.io.IOException;
import java.util.ArrayList;
@@ -21,7 +20,6 @@ public class AsyncWriterPool implements Closeable {
private final ExecutorService executor;
private final List> writers = new ArrayList<>();
-
// The amount of time to wait on the queue in the event of catastrophic failure in the writer threads.
private int timeoutSeconds = 5;
@@ -65,7 +63,10 @@ public AsyncWriterPool() {
public void close() throws IOException {
if (this.poolClosed) return;
this.poolClosed = true;
- CompletableFuture.allOf(this.writers.stream().map(PooledWriter::nonBlockingClose).toArray(CompletableFuture[]::new)).join();
+ CompletableFuture.allOf(this.writers.stream()
+ .map(PooledWriter::nonBlockingClose)
+ .toArray(CompletableFuture[]::new))
+ .join();
this.executor.shutdown();
}
@@ -104,7 +105,6 @@ public Writer pool(final Writer writer, final BlockingQueue queue,
return pooledWriter;
}
-
/**
* Any class that implements {@link Writer} can be exchanged for a {@code PooledWriter}. The PooledWriter provides
* the same API as {@link Writer}, but will manage buffering of writes and sending to the {@link AsyncWriterPool} it
@@ -122,7 +122,8 @@ private class PooledWriter implements Writer {
private boolean isClosed = false;
- // Holds the Future of the last task submitted to the AsyncWriterPools until it is checked, then it is null again.
+ // Holds the Future of the last task submitted to the AsyncWriterPools until it is checked, then it is null
+ // again.
private Future currentTask;
/**
@@ -137,7 +138,8 @@ private PooledWriter(final Writer writer, final BlockingQueue queue, final
if (writeThreshold <= 0)
throw new IllegalArgumentException("writeThreshold must be >= 1: " + writeThreshold);
if (writeThreshold > queue.remainingCapacity())
- throw new IllegalArgumentException("writeThreshold (" + writeThreshold + ") can't be larger then queue capacity (" + queue.remainingCapacity() + ").");
+ throw new IllegalArgumentException("writeThreshold (" + writeThreshold
+ + ") can't be larger then queue capacity (" + queue.remainingCapacity() + ").");
this.writer = writer;
this.queue = queue;
@@ -208,7 +210,10 @@ public void write(final A item) {
* normal operations the timeout should not come into play and items will add immediately.
*/
try {
- while (!this.isClosed && !this.queue.offer(item, AsyncWriterPool.this.getTimeoutSeconds(), TimeUnit.SECONDS)) { /* Just wait. */ }
+ while (!this.isClosed
+ && !this.queue.offer(item, AsyncWriterPool.this.getTimeoutSeconds(), TimeUnit.SECONDS)) {
+ /* Just wait. */
+ }
} catch (InterruptedException e) {
throw new RuntimeException("Exception while placing item in queue", e);
}
@@ -251,14 +256,16 @@ private void drain() {
*/
private CompletableFuture nonBlockingClose() {
- return CompletableFuture.supplyAsync(() -> {
- try {
- this.close();
- return null;
- } catch (Exception e) {
- throw new RuntimeException("Caught exception while closing PooledWriter.", e);
- }
- }, AsyncWriterPool.this.executor);
+ return CompletableFuture.supplyAsync(
+ () -> {
+ try {
+ this.close();
+ return null;
+ } catch (Exception e) {
+ throw new RuntimeException("Caught exception while closing PooledWriter.", e);
+ }
+ },
+ AsyncWriterPool.this.executor);
}
/**
diff --git a/src/main/java/htsjdk/io/HtsPath.java b/src/main/java/htsjdk/io/HtsPath.java
index 035b1ff418..f3c2df78b8 100644
--- a/src/main/java/htsjdk/io/HtsPath.java
+++ b/src/main/java/htsjdk/io/HtsPath.java
@@ -1,7 +1,6 @@
package htsjdk.io;
import htsjdk.utils.ValidationUtils;
-
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
@@ -71,10 +70,10 @@ public class HtsPath implements IOPath, Serializable {
private static final long serialVersionUID = 1L;
private static final String HIERARCHICAL_SCHEME_SEPARATOR = "://";
- private final String rawInputString; // raw input string provided by th user; may or may not have a scheme
- private final URI uri; // working URI; always has a scheme ("file" if not otherwise specified)
+ private final String rawInputString; // raw input string provided by th user; may or may not have a scheme
+ private final URI uri; // working URI; always has a scheme ("file" if not otherwise specified)
private transient String pathFailureReason; // cache the reason for "toPath" conversion failure
- private transient Path cachedPath; // cache the Path associated with this URI if its "Path-able"
+ private transient Path cachedPath; // cache the Path associated with this URI if its "Path-able"
/**
* Create an HtsPath from a raw input path string.
@@ -117,12 +116,14 @@ public String getURIString() {
* Return the raw input string provided to the constructor.
*/
@Override
- public String getRawInputString() { return rawInputString; }
+ public String getRawInputString() {
+ return rawInputString;
+ }
@Override
public boolean hasFileSystemProvider() {
// try to find a provider; assume that our URI always has a scheme
- for (FileSystemProvider provider: FileSystemProvider.installedProviders()) {
+ for (FileSystemProvider provider : FileSystemProvider.installedProviders()) {
if (provider.getScheme().equalsIgnoreCase(uri.getScheme())) {
return true;
}
@@ -134,10 +135,10 @@ public boolean hasFileSystemProvider() {
public boolean isPath() {
try {
return getCachedPath() != null || toPath() != null;
- } catch (ProviderNotFoundException |
- FileSystemNotFoundException |
- IllegalArgumentException |
- AssertionError e) {
+ } catch (ProviderNotFoundException
+ | FileSystemNotFoundException
+ | IllegalArgumentException
+ | AssertionError e) {
// jimfs throws an AssertionError that wraps a URISyntaxException when trying to create path where
// the scheme-specific part is missing or incorrect
pathFailureReason = e.getMessage();
@@ -192,7 +193,10 @@ public InputStream getInputStream() {
return Files.newInputStream(resourcePath);
} catch (IOException e) {
throw new RuntimeException(
- String.format("Could not create open input stream for %s (as URI %s)", getRawInputString(), getURIString()), e);
+ String.format(
+ "Could not create open input stream for %s (as URI %s)",
+ getRawInputString(), getURIString()),
+ e);
}
}
@@ -206,12 +210,17 @@ public OutputStream getOutputStream() {
try {
return Files.newOutputStream(resourcePath);
} catch (IOException e) {
- throw new RuntimeException(String.format("Could not open output stream for %s (as URI %s)", getRawInputString(), getURIString()), e);
+ throw new RuntimeException(
+ String.format(
+ "Could not open output stream for %s (as URI %s)", getRawInputString(), getURIString()),
+ e);
}
}
// get the cached path associated with this URI if its already been created
- protected Path getCachedPath() { return cachedPath; }
+ protected Path getCachedPath() {
+ return cachedPath;
+ }
protected void setCachedPath(Path path) {
this.cachedPath = path;
@@ -251,8 +260,8 @@ private URI getURIForString(final String pathString) {
tempURI = getCachedPath().toUri();
}
} catch (URISyntaxException uriException) {
- //check that the uri wasn't a badly encoded absolute uri of some sort
- //if you don't do this it will be treated as a badly formed file:// url
+ // check that the uri wasn't a badly encoded absolute uri of some sort
+ // if you don't do this it will be treated as a badly formed file:// url
assertNoProblematicScheme(pathString, uriException);
// the input string isn't a valid URI; assume its a local (non-URI) file reference, and
@@ -265,9 +274,7 @@ private URI getURIForString(final String pathString) {
// the user intended to provide a local file reference or a URI, so preserve both
final String errorMessage = String.format(
"%s can't be interpreted as a local file (%s) or as a URI (%s).",
- pathString,
- pathException.getMessage(),
- uriException.getMessage());
+ pathString, pathException.getMessage(), uriException.getMessage());
throw new IllegalArgumentException(errorMessage, pathException);
}
}
@@ -292,28 +299,30 @@ private URI getURIForString(final String pathString) {
* @param pathString the path being examined
* @param cause the original failure reason
*/
- static void assertNoProblematicScheme(String pathString, URISyntaxException cause){
- if(pathString.equals(HIERARCHICAL_SCHEME_SEPARATOR)){
+ static void assertNoProblematicScheme(String pathString, URISyntaxException cause) {
+ if (pathString.equals(HIERARCHICAL_SCHEME_SEPARATOR)) {
throw new IllegalArgumentException(HIERARCHICAL_SCHEME_SEPARATOR + " is not a valid path.", cause);
}
final String[] split = pathString.split(HIERARCHICAL_SCHEME_SEPARATOR, -1);
final String scheme = split[0];
- if(split.length == 2 && pathString.endsWith(HIERARCHICAL_SCHEME_SEPARATOR)) {
- throw new IllegalArgumentException("A path consisting of only a scheme is not allowed: " + pathString, cause);
+ if (split.length == 2 && pathString.endsWith(HIERARCHICAL_SCHEME_SEPARATOR)) {
+ throw new IllegalArgumentException(
+ "A path consisting of only a scheme is not allowed: " + pathString, cause);
}
- if(split.length > 1){
- if(scheme == null || scheme.isEmpty()){
- throw new IllegalArgumentException("Malformed path " + pathString + " includes an empty scheme.", cause);
+ if (split.length > 1) {
+ if (scheme == null || scheme.isEmpty()) {
+ throw new IllegalArgumentException(
+ "Malformed path " + pathString + " includes an empty scheme.", cause);
}
- if(!scheme.equals("file")){
- throw new IllegalArgumentException("Malformed path " + pathString + " includes a scheme: " + scheme + ":// but was an invalid URI." +
- "\nCheck that it is fully encoded.", cause);
+ if (!scheme.equals("file")) {
+ throw new IllegalArgumentException(
+ "Malformed path " + pathString + " includes a scheme: " + scheme + ":// but was an invalid URI."
+ + "\nCheck that it is fully encoded.",
+ cause);
}
}
-
}
-
}
diff --git a/src/main/java/htsjdk/io/IOPath.java b/src/main/java/htsjdk/io/IOPath.java
index 7f22df3c4a..bd2d3d1873 100644
--- a/src/main/java/htsjdk/io/IOPath.java
+++ b/src/main/java/htsjdk/io/IOPath.java
@@ -2,7 +2,6 @@
import htsjdk.samtools.util.FileExtensions;
import htsjdk.utils.ValidationUtils;
-
import java.io.InputStream;
import java.io.OutputStream;
import java.net.URI;
@@ -91,7 +90,8 @@ default String getScheme() {
default Optional getExtension() {
final String hierarchicalPath = getURI().getPath();
if (hierarchicalPath != null) {
- final int indexOfLastComponent = hierarchicalPath.lastIndexOf(FileSystems.getDefault().getSeparator());
+ final int indexOfLastComponent =
+ hierarchicalPath.lastIndexOf(FileSystems.getDefault().getSeparator());
if (indexOfLastComponent != -1 && indexOfLastComponent < hierarchicalPath.length() - 1) {
final String lastComponent = hierarchicalPath.substring(indexOfLastComponent + 1);
if (lastComponent.length() > 0) {
@@ -127,9 +127,7 @@ default boolean hasExtension(final String extension) {
// We don't want to use {@code #getExtension} here, since it won't work correctly if we're comparing an
// extension that uses multiple . chars, such as .fasta.gz.
final String hierarchicalPath = getURI().getPath();
- return hierarchicalPath == null ?
- false :
- hierarchicalPath.toLowerCase().endsWith(extension.toLowerCase());
+ return hierarchicalPath == null ? false : hierarchicalPath.toLowerCase().endsWith(extension.toLowerCase());
}
/**
@@ -140,7 +138,8 @@ default boolean hasExtension(final String extension) {
*/
default Optional getBaseName() {
final String hierarchicalPath = getURI().getPath();
- final int indexOfLastComponent = hierarchicalPath.lastIndexOf(FileSystems.getDefault().getSeparator());
+ final int indexOfLastComponent =
+ hierarchicalPath.lastIndexOf(FileSystems.getDefault().getSeparator());
if (indexOfLastComponent != -1 && indexOfLastComponent < hierarchicalPath.length() - 1) {
final String lastComponent = hierarchicalPath.substring(indexOfLastComponent + 1);
if (lastComponent.length() > 0) {
diff --git a/src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java b/src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java
index 9df206ecfd..7989ca3184 100644
--- a/src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java
+++ b/src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java
@@ -25,7 +25,6 @@
import htsjdk.samtools.seekablestream.SeekableStream;
import htsjdk.samtools.util.RuntimeIOException;
-
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
@@ -60,11 +59,16 @@ protected AbstractBAMFileIndex(final File file, final SAMSequenceDictionary dict
this(new MemoryMappedFileBuffer(file), file.getName(), dictionary);
}
- protected AbstractBAMFileIndex(final File file, final SAMSequenceDictionary dictionary, final boolean useMemoryMapping) {
- this((useMemoryMapping ? new MemoryMappedFileBuffer(file) : new RandomAccessFileBuffer(file)), file.getName(), dictionary);
+ protected AbstractBAMFileIndex(
+ final File file, final SAMSequenceDictionary dictionary, final boolean useMemoryMapping) {
+ this(
+ (useMemoryMapping ? new MemoryMappedFileBuffer(file) : new RandomAccessFileBuffer(file)),
+ file.getName(),
+ dictionary);
}
- protected AbstractBAMFileIndex(final IndexFileBuffer indexFileBuffer, final String source, final SAMSequenceDictionary dictionary) {
+ protected AbstractBAMFileIndex(
+ final IndexFileBuffer indexFileBuffer, final String source, final SAMSequenceDictionary dictionary) {
mIndexBuffer = indexFileBuffer;
mBamDictionary = dictionary;
verifyIndexMagicNumber(source);
@@ -87,9 +91,10 @@ public static int getNumIndexLevels() {
return GenomicIndexUtil.LEVEL_STARTS.length;
}
- private static void assertLevelIsValid (final int levelNumber) {
+ private static void assertLevelIsValid(final int levelNumber) {
if (levelNumber >= getNumIndexLevels()) {
- throw new SAMException("Level number (" + levelNumber + ") is greater than or equal to maximum (" + getNumIndexLevels() + ").");
+ throw new SAMException("Level number (" + levelNumber + ") is greater than or equal to maximum ("
+ + getNumIndexLevels() + ").");
}
}
@@ -112,7 +117,7 @@ public static int getFirstBinInLevel(final int levelNumber) {
public int getLevelSize(final int levelNumber) {
assertLevelIsValid(levelNumber);
- if (levelNumber == getNumIndexLevels()-1) {
+ if (levelNumber == getNumIndexLevels() - 1) {
return GenomicIndexUtil.MAX_BINS - GenomicIndexUtil.LEVEL_STARTS[levelNumber] - 1;
} else {
return GenomicIndexUtil.LEVEL_STARTS[levelNumber + 1] - GenomicIndexUtil.LEVEL_STARTS[levelNumber];
@@ -125,13 +130,12 @@ public int getLevelSize(final int levelNumber) {
* @return the level associated with the given bin number.
*/
public int getLevelForBin(final Bin bin) {
- if(bin.getBinNumber() >= GenomicIndexUtil.MAX_BINS)
+ if (bin.getBinNumber() >= GenomicIndexUtil.MAX_BINS)
throw new SAMException("Tried to get level for invalid bin.");
- for(int i = getNumIndexLevels()-1; i >= 0; i--) {
- if(bin.getBinNumber() >= GenomicIndexUtil.LEVEL_STARTS[i])
- return i;
+ for (int i = getNumIndexLevels() - 1; i >= 0; i--) {
+ if (bin.getBinNumber() >= GenomicIndexUtil.LEVEL_STARTS[i]) return i;
}
- throw new SAMException("Unable to find correct bin for bin "+bin);
+ throw new SAMException("Unable to find correct bin for bin " + bin);
}
/**
@@ -142,8 +146,11 @@ public int getLevelForBin(final Bin bin) {
public int getFirstLocusInBin(final Bin bin) {
final int level = getLevelForBin(bin);
final int levelStart = GenomicIndexUtil.LEVEL_STARTS[level];
- final int levelSize = ((level==getNumIndexLevels()-1) ? GenomicIndexUtil.MAX_BINS-1 : GenomicIndexUtil.LEVEL_STARTS[level+1]) - levelStart;
- return (bin.getBinNumber() - levelStart)*(GenomicIndexUtil.BIN_GENOMIC_SPAN /levelSize)+1;
+ final int levelSize = ((level == getNumIndexLevels() - 1)
+ ? GenomicIndexUtil.MAX_BINS - 1
+ : GenomicIndexUtil.LEVEL_STARTS[level + 1])
+ - levelStart;
+ return (bin.getBinNumber() - levelStart) * (GenomicIndexUtil.BIN_GENOMIC_SPAN / levelSize) + 1;
}
/**
@@ -154,8 +161,11 @@ public int getFirstLocusInBin(final Bin bin) {
public int getLastLocusInBin(final Bin bin) {
final int level = getLevelForBin(bin);
final int levelStart = GenomicIndexUtil.LEVEL_STARTS[level];
- final int levelSize = ((level==getNumIndexLevels()-1) ? GenomicIndexUtil.MAX_BINS-1 : GenomicIndexUtil.LEVEL_STARTS[level+1]) - levelStart;
- return (bin.getBinNumber()-levelStart+1)*(GenomicIndexUtil.BIN_GENOMIC_SPAN /levelSize);
+ final int levelSize = ((level == getNumIndexLevels() - 1)
+ ? GenomicIndexUtil.MAX_BINS - 1
+ : GenomicIndexUtil.LEVEL_STARTS[level + 1])
+ - levelStart;
+ return (bin.getBinNumber() - levelStart + 1) * (GenomicIndexUtil.BIN_GENOMIC_SPAN / levelSize);
}
public int getNumberOfReferences() {
@@ -271,7 +281,7 @@ protected BAMIndexContent query(final int referenceSequence, final int startPos,
final int binCount = readInteger();
boolean metaDataSeen = false;
- final Bin[] bins = new Bin[getMaxBinNumberForReference(referenceSequence) +1];
+ final Bin[] bins = new Bin[getMaxBinNumberForReference(referenceSequence) + 1];
for (int binNumber = 0; binNumber < binCount; binNumber++) {
final int indexBin = readInteger();
final int nChunks = readInteger();
@@ -279,7 +289,7 @@ protected BAMIndexContent query(final int referenceSequence, final int startPos,
// System.out.println("# bin[" + i + "] = " + indexBin + ", nChunks = " + nChunks);
Chunk lastChunk = null;
if (regionBins.get(indexBin)) {
- chunks = new ArrayList(nChunks);
+ chunks = new ArrayList(nChunks);
readChunks(nChunks, chunks);
} else if (indexBin == GenomicIndexUtil.MAX_BINS) {
// meta data - build the bin so that the count of bins is correct;
@@ -300,20 +310,25 @@ protected BAMIndexContent query(final int referenceSequence, final int startPos,
final int nLinearBins = readInteger();
final int regionLinearBinStart = LinearIndex.convertToLinearIndexOffset(startPos);
- final int regionLinearBinStop = endPos > 0 ? LinearIndex.convertToLinearIndexOffset(endPos) : nLinearBins-1;
- final int actualStop = Math.min(regionLinearBinStop, nLinearBins -1);
+ final int regionLinearBinStop = endPos > 0 ? LinearIndex.convertToLinearIndexOffset(endPos) : nLinearBins - 1;
+ final int actualStop = Math.min(regionLinearBinStop, nLinearBins - 1);
long[] linearIndexEntries = new long[0];
if (regionLinearBinStart < nLinearBins) {
- linearIndexEntries = new long[actualStop-regionLinearBinStart+1];
+ linearIndexEntries = new long[actualStop - regionLinearBinStart + 1];
skipBytes(8 * regionLinearBinStart);
- for(int linearBin = regionLinearBinStart; linearBin <= actualStop; linearBin++)
- linearIndexEntries[linearBin-regionLinearBinStart] = readLong();
+ for (int linearBin = regionLinearBinStart; linearBin <= actualStop; linearBin++)
+ linearIndexEntries[linearBin - regionLinearBinStart] = readLong();
}
- final LinearIndex linearIndex = new LinearIndex(referenceSequence,regionLinearBinStart,linearIndexEntries);
+ final LinearIndex linearIndex = new LinearIndex(referenceSequence, regionLinearBinStart, linearIndexEntries);
- return new BAMIndexContent(referenceSequence, bins, binCount - (metaDataSeen? 1 : 0), new BAMIndexMetaData(metaDataChunks), linearIndex);
+ return new BAMIndexContent(
+ referenceSequence,
+ bins,
+ binCount - (metaDataSeen ? 1 : 0),
+ new BAMIndexMetaData(metaDataChunks),
+ linearIndex);
}
/**
@@ -338,7 +353,7 @@ static int getMaxBinNumberForSequenceLength(final int sequenceLength) {
// return 4680 + (sequenceLength >> 14); // note 4680 = getFirstBinInLevel(getNumIndexLevels() - 1)
}
- abstract protected BAMIndexContent getQueryResults(int reference);
+ protected abstract BAMIndexContent getQueryResults(int reference);
/**
* Gets the possible number of bins for a given reference sequence.
@@ -375,8 +390,7 @@ protected void verifyIndexMagicNumber(final String sourceName) {
final byte[] buffer = new byte[4];
readBytes(buffer);
if (!Arrays.equals(buffer, BAMFileConstants.BAI_INDEX_MAGIC)) {
- throw new RuntimeIOException("Invalid file header in BAM index " + sourceName +
- ": " + new String(buffer));
+ throw new RuntimeIOException("Invalid file header in BAM index " + sourceName + ": " + new String(buffer));
}
}
@@ -399,11 +413,11 @@ protected void readChunks(int nChunks, List chunks) {
}
protected void skipToSequence(final int sequenceIndex) {
- //Use sequence position cache if available
- if(sequenceIndexes[sequenceIndex] != -1){
- seek(sequenceIndexes[sequenceIndex]);
- return;
- }
+ // Use sequence position cache if available
+ if (sequenceIndexes[sequenceIndex] != -1) {
+ seek(sequenceIndexes[sequenceIndex]);
+ return;
+ }
// Use previous sequence position if in cache, which optimizes for common access pattern
// of iterating through sequences in order.
@@ -415,7 +429,7 @@ protected void skipToSequence(final int sequenceIndex) {
} else {
startSequenceIndex = 0;
}
-
+
for (int i = startSequenceIndex; i < sequenceIndex; i++) {
// System.out.println("# Sequence TID: " + i);
final int nBins = readInteger();
@@ -430,8 +444,8 @@ protected void skipToSequence(final int sequenceIndex) {
// System.out.println("# nLinearBins: " + nLinearBins);
skipBytes(8 * nLinearBins);
}
-
- //Update sequence position cache
+
+ // Update sequence position cache
sequenceIndexes[sequenceIndex] = position();
}
@@ -454,16 +468,16 @@ protected final void skipBytes(final int count) {
protected final void seek(final long position) {
mIndexBuffer.seek(position);
}
-
- protected final long position(){
- return mIndexBuffer.position();
+
+ protected final long position() {
+ return mIndexBuffer.position();
}
protected final SAMSequenceDictionary getBamDictionary() {
return mBamDictionary;
}
- protected final void setSequenceIndexes (int nReferences) {
+ protected final void setSequenceIndexes(int nReferences) {
sequenceIndexes = new long[nReferences + 1];
Arrays.fill(sequenceIndexes, -1);
}
diff --git a/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java b/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java
index a3e2ce5966..210d2e0415 100644
--- a/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java
+++ b/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java
@@ -23,7 +23,6 @@
*/
package htsjdk.samtools;
-
import java.io.Serializable;
import java.util.LinkedHashMap;
import java.util.Map;
@@ -33,11 +32,10 @@
* Base class for the various concrete records in a SAM header, providing uniform
* access to the attributes.
*/
-
public abstract class AbstractSAMHeaderRecord implements Serializable {
public static final long serialVersionUID = 1L;
- private final Map mAttributes = new LinkedHashMap();
+ private final Map mAttributes = new LinkedHashMap();
public String getAttribute(final String key) {
return mAttributes.get(key);
@@ -53,7 +51,7 @@ public String getAttribute(final String key) {
*/
@Deprecated
public void setAttribute(final String key, final Object value) {
- setAttribute(key, value == null? null: value.toString());
+ setAttribute(key, value == null ? null : value.toString());
}
/**
@@ -83,11 +81,10 @@ public void setAttribute(final String key, final String value) {
/**
* Returns the Set of attributes.
*/
- public Set> getAttributes() {
+ public Set> getAttributes() {
return mAttributes.entrySet();
}
-
/**
* Returns the ID tag (or equivalent) for this header record. The
* default implementation throws a SAMException to indicate "not implemented".
@@ -118,7 +115,8 @@ protected int attributesHashCode() {
abstract Set getStandardTags();
/** Simple to String that outputs the concrete class name and the set of attributes stored. */
- @Override public String toString() {
+ @Override
+ public String toString() {
return getClass().getSimpleName() + this.mAttributes.toString();
}
@@ -126,5 +124,5 @@ protected int attributesHashCode() {
* Returns the record in the SAM line-based text format. Fields are
* separated by '\t' characters. The String is NOT terminated by '\n'.
*/
- abstract public String getSAMString();
+ public abstract String getSAMString();
}
diff --git a/src/main/java/htsjdk/samtools/AlignmentBlock.java b/src/main/java/htsjdk/samtools/AlignmentBlock.java
index 1320dfdf66..bf41783ff3 100644
--- a/src/main/java/htsjdk/samtools/AlignmentBlock.java
+++ b/src/main/java/htsjdk/samtools/AlignmentBlock.java
@@ -48,11 +48,17 @@ public class AlignmentBlock implements Serializable {
}
/** The first, 1-based, base in the read that is aligned to the reference reference. */
- public int getReadStart() { return readStart; }
+ public int getReadStart() {
+ return readStart;
+ }
/** The first, 1-based, position in the reference to which the read is aligned. */
- public int getReferenceStart() { return referenceStart; }
+ public int getReferenceStart() {
+ return referenceStart;
+ }
/** The number of contiguous bases aligned to the reference. */
- public int getLength() { return length; }
+ public int getLength() {
+ return length;
+ }
}
diff --git a/src/main/java/htsjdk/samtools/AsyncSAMFileWriter.java b/src/main/java/htsjdk/samtools/AsyncSAMFileWriter.java
index ea85458ec3..3d8e0f561c 100644
--- a/src/main/java/htsjdk/samtools/AsyncSAMFileWriter.java
+++ b/src/main/java/htsjdk/samtools/AsyncSAMFileWriter.java
@@ -33,16 +33,25 @@ public AsyncSAMFileWriter(final SAMFileWriter out, final int queueSize) {
this.underlyingWriter = out;
}
- @Override protected void synchronouslyWrite(final SAMRecord item) { this.underlyingWriter.addAlignment(item); }
+ @Override
+ protected void synchronouslyWrite(final SAMRecord item) {
+ this.underlyingWriter.addAlignment(item);
+ }
- @Override protected void synchronouslyClose() { this.underlyingWriter.close(); }
+ @Override
+ protected void synchronouslyClose() {
+ this.underlyingWriter.close();
+ }
- @Override protected final String getThreadNamePrefix() { return "SAMFileWriterThread-"; }
+ @Override
+ protected final String getThreadNamePrefix() {
+ return "SAMFileWriterThread-";
+ }
- @Override
- public void setProgressLogger(final ProgressLoggerInterface progress) {
- this.underlyingWriter.setProgressLogger(progress);
- }
+ @Override
+ public void setProgressLogger(final ProgressLoggerInterface progress) {
+ this.underlyingWriter.setProgressLogger(progress);
+ }
@Override
public void setSortOrderChecking(boolean check) {
diff --git a/src/main/java/htsjdk/samtools/BAMFileConstants.java b/src/main/java/htsjdk/samtools/BAMFileConstants.java
index 638c56cc56..8192bf5612 100644
--- a/src/main/java/htsjdk/samtools/BAMFileConstants.java
+++ b/src/main/java/htsjdk/samtools/BAMFileConstants.java
@@ -36,7 +36,6 @@ class BAMFileConstants {
* BAM file magic number. This is what is present in the gunzipped version of the file,
* which never exists on disk.
*/
-
static final byte[] BAM_MAGIC = "BAM\1".getBytes();
/**
* BAM index file magic numbers.
@@ -44,6 +43,7 @@ class BAMFileConstants {
*/
@Deprecated
static final byte[] BAM_INDEX_MAGIC = "BAI\1".getBytes();
+
static final byte[] BAI_INDEX_MAGIC = "BAI\1".getBytes();
static final byte[] CSI_INDEX_MAGIC = "CSI\1".getBytes();
@@ -51,6 +51,7 @@ class BAMFileConstants {
* CSI index related constants
*/
static final int CSI_MAGIC_OFFSET = 0;
+
static final int CSI_MINSHIFT_OFFSET = 4;
static final int CSI_AUXDATA_OFFSET = 12;
static final int CSI_CHUNK_SIZE = 16;
diff --git a/src/main/java/htsjdk/samtools/BAMFileReader.java b/src/main/java/htsjdk/samtools/BAMFileReader.java
index 3693eeba8c..9667174d32 100644
--- a/src/main/java/htsjdk/samtools/BAMFileReader.java
+++ b/src/main/java/htsjdk/samtools/BAMFileReader.java
@@ -23,11 +23,9 @@
*/
package htsjdk.samtools;
-
import htsjdk.samtools.seekablestream.SeekableStream;
import htsjdk.samtools.util.*;
import htsjdk.samtools.util.zip.InflaterFactory;
-
import java.io.DataInputStream;
import java.io.File;
import java.io.IOException;
@@ -94,15 +92,22 @@ public class BAMFileReader extends SamReader.ReaderImplementation {
* @param samRecordFactory SAM record factory
* @throws IOException
*/
- BAMFileReader(final InputStream stream,
- final File indexFile,
- final boolean eagerDecode,
- final boolean useAsynchronousIO,
- final ValidationStringency validationStringency,
- final SAMRecordFactory samRecordFactory)
+ BAMFileReader(
+ final InputStream stream,
+ final File indexFile,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory)
throws IOException {
- this(stream, indexFile, eagerDecode, useAsynchronousIO, validationStringency, samRecordFactory,
- BlockGunzipper.getDefaultInflaterFactory());
+ this(
+ stream,
+ indexFile,
+ eagerDecode,
+ useAsynchronousIO,
+ validationStringency,
+ samRecordFactory,
+ BlockGunzipper.getDefaultInflaterFactory());
}
/**
@@ -116,17 +121,20 @@ public class BAMFileReader extends SamReader.ReaderImplementation {
* @param inflaterFactory InflaterFactory used by BlockCompressedInputStream
* @throws IOException
*/
- BAMFileReader(final InputStream stream,
- final File indexFile,
- final boolean eagerDecode,
- final boolean useAsynchronousIO,
- final ValidationStringency validationStringency,
- final SAMRecordFactory samRecordFactory,
- final InflaterFactory inflaterFactory)
+ BAMFileReader(
+ final InputStream stream,
+ final File indexFile,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory,
+ final InflaterFactory inflaterFactory)
throws IOException {
mIndexFile = indexFile;
mIsSeekable = false;
- mCompressedInputStream = useAsynchronousIO ? new AsyncBlockCompressedInputStream(stream, inflaterFactory) : new BlockCompressedInputStream(stream, inflaterFactory);
+ mCompressedInputStream = useAsynchronousIO
+ ? new AsyncBlockCompressedInputStream(stream, inflaterFactory)
+ : new BlockCompressedInputStream(stream, inflaterFactory);
mStream = new BinaryCodec(new DataInputStream(mCompressedInputStream));
this.eagerDecode = eagerDecode;
this.mValidationStringency = validationStringency;
@@ -144,14 +152,22 @@ public class BAMFileReader extends SamReader.ReaderImplementation {
* @param samRecordFactory SAM record factory
* @throws IOException
*/
- BAMFileReader(final File file,
- final File indexFile,
- final boolean eagerDecode,
- final boolean useAsynchronousIO,
- final ValidationStringency validationStringency,
- final SAMRecordFactory samRecordFactory)
- throws IOException {
- this(file, indexFile, eagerDecode, useAsynchronousIO, validationStringency, samRecordFactory, BlockGunzipper.getDefaultInflaterFactory());
+ BAMFileReader(
+ final File file,
+ final File indexFile,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory)
+ throws IOException {
+ this(
+ file,
+ indexFile,
+ eagerDecode,
+ useAsynchronousIO,
+ validationStringency,
+ samRecordFactory,
+ BlockGunzipper.getDefaultInflaterFactory());
}
/**
@@ -165,20 +181,29 @@ public class BAMFileReader extends SamReader.ReaderImplementation {
* @param inflaterFactory InflaterFactory used by BlockCompressedInputStream
* @throws IOException
*/
- BAMFileReader(final File file,
- final File indexFile,
- final boolean eagerDecode,
- final boolean useAsynchronousIO,
- final ValidationStringency validationStringency,
- final SAMRecordFactory samRecordFactory,
- final InflaterFactory inflaterFactory)
- throws IOException {
- this(useAsynchronousIO ? new AsyncBlockCompressedInputStream(file, inflaterFactory) : new BlockCompressedInputStream(file, inflaterFactory),
- indexFile!=null ? indexFile : SamFiles.findIndex(file), eagerDecode, useAsynchronousIO, file.getAbsolutePath(), validationStringency, samRecordFactory);
+ BAMFileReader(
+ final File file,
+ final File indexFile,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory,
+ final InflaterFactory inflaterFactory)
+ throws IOException {
+ this(
+ useAsynchronousIO
+ ? new AsyncBlockCompressedInputStream(file, inflaterFactory)
+ : new BlockCompressedInputStream(file, inflaterFactory),
+ indexFile != null ? indexFile : SamFiles.findIndex(file),
+ eagerDecode,
+ useAsynchronousIO,
+ file.getAbsolutePath(),
+ validationStringency,
+ samRecordFactory);
if (mIndexFile != null && mIndexFile.lastModified() < file.lastModified() - 5000) {
- System.err.println("WARNING: BAM index file " + mIndexFile.getAbsolutePath() +
- " is older than BAM " + file.getAbsolutePath());
+ System.err.println("WARNING: BAM index file " + mIndexFile.getAbsolutePath() + " is older than BAM "
+ + file.getAbsolutePath());
}
// Provide better error message when there is an error reading.
@@ -195,14 +220,22 @@ public class BAMFileReader extends SamReader.ReaderImplementation {
* @param samRecordFactory SAM record factory
* @throws IOException
*/
- BAMFileReader(final SeekableStream strm,
- final File indexFile,
- final boolean eagerDecode,
- final boolean useAsynchronousIO,
- final ValidationStringency validationStringency,
- final SAMRecordFactory samRecordFactory)
- throws IOException {
- this(strm, indexFile, eagerDecode, useAsynchronousIO, validationStringency, samRecordFactory, BlockGunzipper.getDefaultInflaterFactory());
+ BAMFileReader(
+ final SeekableStream strm,
+ final File indexFile,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory)
+ throws IOException {
+ this(
+ strm,
+ indexFile,
+ eagerDecode,
+ useAsynchronousIO,
+ validationStringency,
+ samRecordFactory,
+ BlockGunzipper.getDefaultInflaterFactory());
}
/**
@@ -216,16 +249,25 @@ public class BAMFileReader extends SamReader.ReaderImplementation {
* @param inflaterFactory InflaterFactory used by BlockCompressedInputStream
* @throws IOException
*/
- BAMFileReader(final SeekableStream strm,
- final File indexFile,
- final boolean eagerDecode,
- final boolean useAsynchronousIO,
- final ValidationStringency validationStringency,
- final SAMRecordFactory samRecordFactory,
- final InflaterFactory inflaterFactory)
- throws IOException {
- this(useAsynchronousIO ? new AsyncBlockCompressedInputStream(strm, inflaterFactory) : new BlockCompressedInputStream(strm, inflaterFactory),
- indexFile, eagerDecode, useAsynchronousIO, strm.getSource(), validationStringency, samRecordFactory);
+ BAMFileReader(
+ final SeekableStream strm,
+ final File indexFile,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory,
+ final InflaterFactory inflaterFactory)
+ throws IOException {
+ this(
+ useAsynchronousIO
+ ? new AsyncBlockCompressedInputStream(strm, inflaterFactory)
+ : new BlockCompressedInputStream(strm, inflaterFactory),
+ indexFile,
+ eagerDecode,
+ useAsynchronousIO,
+ strm.getSource(),
+ validationStringency,
+ samRecordFactory);
}
/**
@@ -238,14 +280,22 @@ public class BAMFileReader extends SamReader.ReaderImplementation {
* @param samRecordFactory SAM record factory
* @throws IOException
*/
- BAMFileReader(final SeekableStream strm,
- final SeekableStream indexStream,
- final boolean eagerDecode,
- final boolean useAsynchronousIO,
- final ValidationStringency validationStringency,
- final SAMRecordFactory samRecordFactory)
- throws IOException {
- this(strm, indexStream, eagerDecode, useAsynchronousIO, validationStringency, samRecordFactory, BlockGunzipper.getDefaultInflaterFactory());
+ BAMFileReader(
+ final SeekableStream strm,
+ final SeekableStream indexStream,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory)
+ throws IOException {
+ this(
+ strm,
+ indexStream,
+ eagerDecode,
+ useAsynchronousIO,
+ validationStringency,
+ samRecordFactory,
+ BlockGunzipper.getDefaultInflaterFactory());
}
/**
@@ -259,16 +309,25 @@ public class BAMFileReader extends SamReader.ReaderImplementation {
* @param inflaterFactory InflaterFactory used by BlockCompressedInputStream
* @throws IOException
*/
- BAMFileReader(final SeekableStream strm,
- final SeekableStream indexStream,
- final boolean eagerDecode,
- final boolean useAsynchronousIO,
- final ValidationStringency validationStringency,
- final SAMRecordFactory samRecordFactory,
- final InflaterFactory inflaterFactory)
- throws IOException {
- this(useAsynchronousIO ? new AsyncBlockCompressedInputStream(strm, inflaterFactory) : new BlockCompressedInputStream(strm, inflaterFactory),
- indexStream, eagerDecode, useAsynchronousIO, strm.getSource(), validationStringency, samRecordFactory);
+ BAMFileReader(
+ final SeekableStream strm,
+ final SeekableStream indexStream,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory,
+ final InflaterFactory inflaterFactory)
+ throws IOException {
+ this(
+ useAsynchronousIO
+ ? new AsyncBlockCompressedInputStream(strm, inflaterFactory)
+ : new BlockCompressedInputStream(strm, inflaterFactory),
+ indexStream,
+ eagerDecode,
+ useAsynchronousIO,
+ strm.getSource(),
+ validationStringency,
+ samRecordFactory);
}
/**
@@ -282,14 +341,15 @@ public class BAMFileReader extends SamReader.ReaderImplementation {
* @param samRecordFactory SAM record factory
* @throws IOException
*/
- private BAMFileReader(final BlockCompressedInputStream compressedInputStream,
- final File indexFile,
- final boolean eagerDecode,
- final boolean useAsynchronousIO,
- final String source,
- final ValidationStringency validationStringency,
- final SAMRecordFactory samRecordFactory)
- throws IOException {
+ private BAMFileReader(
+ final BlockCompressedInputStream compressedInputStream,
+ final File indexFile,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final String source,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory)
+ throws IOException {
mIndexFile = indexFile;
mIsSeekable = true;
mCompressedInputStream = compressedInputStream;
@@ -312,14 +372,15 @@ private BAMFileReader(final BlockCompressedInputStream compressedInputStream,
* @param samRecordFactory SAM record factory
* @throws IOException
*/
- private BAMFileReader(final BlockCompressedInputStream compressedInputStream,
- final SeekableStream indexStream,
- final boolean eagerDecode,
- final boolean useAsynchronousIO,
- final String source,
- final ValidationStringency validationStringency,
- final SAMRecordFactory samRecordFactory)
- throws IOException {
+ private BAMFileReader(
+ final BlockCompressedInputStream compressedInputStream,
+ final SeekableStream indexStream,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final String source,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory)
+ throws IOException {
mIndexStream = indexStream;
mIsSeekable = true;
mCompressedInputStream = compressedInputStream;
@@ -333,7 +394,8 @@ private BAMFileReader(final BlockCompressedInputStream compressedInputStream,
/** Reads through the header and sequence records to find the virtual file offset of the first record in the BAM file. */
static long findVirtualOffsetOfFirstRecord(final File bam) throws IOException {
- final BAMFileReader reader = new BAMFileReader(bam, null, false, false, ValidationStringency.SILENT, new DefaultSAMRecordFactory());
+ final BAMFileReader reader =
+ new BAMFileReader(bam, null, false, false, ValidationStringency.SILENT, new DefaultSAMRecordFactory());
final long offset = reader.mFirstRecordPointer;
reader.close();
return offset;
@@ -344,7 +406,13 @@ static long findVirtualOffsetOfFirstRecord(final File bam) throws IOException {
* The caller is responsible for closing the stream.
*/
static long findVirtualOffsetOfFirstRecord(final SeekableStream seekableStream) throws IOException {
- final BAMFileReader reader = new BAMFileReader(seekableStream, (SeekableStream) null, false, false, ValidationStringency.SILENT, new DefaultSAMRecordFactory());
+ final BAMFileReader reader = new BAMFileReader(
+ seekableStream,
+ (SeekableStream) null,
+ false,
+ false,
+ ValidationStringency.SILENT,
+ new DefaultSAMRecordFactory());
return reader.mFirstRecordPointer;
}
@@ -363,7 +431,7 @@ void enableFileSource(final SamReader reader, final boolean enabled) {
*/
@Override
protected void enableIndexCaching(final boolean enabled) {
- if(mIndex != null)
+ if (mIndex != null)
throw new SAMException("Unable to turn on index caching; index file has already been loaded.");
this.mEnableIndexCaching = enabled;
}
@@ -381,11 +449,15 @@ protected void enableIndexMemoryMapping(final boolean enabled) {
this.mEnableIndexMemoryMapping = enabled;
}
- @Override void enableCrcChecking(final boolean enabled) {
+ @Override
+ void enableCrcChecking(final boolean enabled) {
this.mCompressedInputStream.setCheckCrcs(enabled);
}
- @Override void setSAMRecordFactory(final SAMRecordFactory samRecordFactory) { this.samRecordFactory = samRecordFactory; }
+ @Override
+ void setSAMRecordFactory(final SAMRecordFactory samRecordFactory) {
+ this.samRecordFactory = samRecordFactory;
+ }
@Override
public SamReader.Type type() {
@@ -409,26 +481,27 @@ public boolean hasIndex() {
*/
@Override
public BAMIndex getIndex() {
- if(!hasIndex()) {
+ if (!hasIndex()) {
throw new SAMException("No index is available for this BAM file.");
}
- if(mIndex == null) {
+ if (mIndex == null) {
final SamIndexes samIndexType = getIndexType();
final SAMSequenceDictionary sequenceDictionary = getFileHeader().getSequenceDictionary();
- if(mIndexFile != null) {
+ if (mIndexFile != null) {
if (samIndexType.equals(SamIndexes.BAI)) {
- mIndex = mEnableIndexCaching ? new CachingBAMFileIndex(mIndexFile, sequenceDictionary, mEnableIndexMemoryMapping)
+ mIndex = mEnableIndexCaching
+ ? new CachingBAMFileIndex(mIndexFile, sequenceDictionary, mEnableIndexMemoryMapping)
: new DiskBasedBAMFileIndex(mIndexFile, sequenceDictionary, mEnableIndexMemoryMapping);
} else if (samIndexType.equals(SamIndexes.CSI)) {
mIndex = new CSIIndex(mIndexFile, mEnableIndexMemoryMapping, sequenceDictionary);
} else {
throw new SAMFormatException("Unsupported BAM index file format: " + mIndexFile.getName());
}
- } else if(mIndexStream != null) {
+ } else if (mIndexStream != null) {
if (samIndexType.equals(SamIndexes.BAI)) {
mIndex = new CachingBAMFileIndex(mIndexStream, sequenceDictionary);
} else if (samIndexType.equals(SamIndexes.CSI)) {
- mIndex = new CSIIndex(mIndexStream, sequenceDictionary);
+ mIndex = new CSIIndex(mIndexStream, sequenceDictionary);
} else {
throw new SAMFormatException("Unsupported BAM index file format: " + mIndexStream.getSource());
}
@@ -455,13 +528,16 @@ public SamIndexes getIndexType() {
if (samIndexesType == SamIndexes.BAI || samIndexesType == SamIndexes.CSI) {
return samIndexesType;
}
- throw new SAMFormatException(String.format("Unknown BAM index file type: %s in %s", samIndexesType, mIndexStream.getSource()));
+ throw new SAMFormatException(
+ String.format("Unknown BAM index file type: %s in %s", samIndexesType, mIndexStream.getSource()));
}
return null;
}
- public void setEagerDecode(final boolean desired) { this.eagerDecode = desired; }
+ public void setEagerDecode(final boolean desired) {
+ this.eagerDecode = desired;
+ }
@Override
public void close() {
@@ -541,7 +617,7 @@ public CloseableIterator getIterator(final SAMFileSpan chunks) {
}
// Create an iterator over the given chunk boundaries.
- mCurrentIterator = new BAMFileIndexIterator(((BAMFileSpan)chunks).toCoordinateArray());
+ mCurrentIterator = new BAMFileIndexIterator(((BAMFileSpan) chunks).toCoordinateArray());
return mCurrentIterator;
}
@@ -553,7 +629,7 @@ public CloseableIterator getIterator(final SAMFileSpan chunks) {
*/
@Override
public SAMFileSpan getFilePointerSpanningReads() {
- return new BAMFileSpan(new Chunk(mFirstRecordPointer,Long.MAX_VALUE));
+ return new BAMFileSpan(new Chunk(mFirstRecordPointer, Long.MAX_VALUE));
}
/**
@@ -704,8 +780,9 @@ public CloseableIterator queryUnmapped() {
* @param validationStringency Determines how stringent to be when validating the sam
* @param source Note that this is used only for reporting errors.
*/
- protected static SAMFileHeader readHeader(final BinaryCodec stream, final ValidationStringency validationStringency, final String source)
- throws IOException {
+ protected static SAMFileHeader readHeader(
+ final BinaryCodec stream, final ValidationStringency validationStringency, final String source)
+ throws IOException {
final byte[] buffer = new byte[4];
stream.readBytes(buffer);
@@ -717,27 +794,27 @@ protected static SAMFileHeader readHeader(final BinaryCodec stream, final Valida
final String textHeader = stream.readString(headerTextLength);
final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec();
headerCodec.setValidationStringency(validationStringency);
- final SAMFileHeader samFileHeader = headerCodec.decode(BufferedLineReader.fromString(textHeader),
- source);
+ final SAMFileHeader samFileHeader = headerCodec.decode(BufferedLineReader.fromString(textHeader), source);
final int sequenceCount = stream.readInt();
if (!samFileHeader.getSequenceDictionary().isEmpty()) {
// It is allowed to have binary sequences but no text sequences, so only validate if both are present
if (sequenceCount != samFileHeader.getSequenceDictionary().size()) {
- throw new SAMFormatException("Number of sequences in text header (" +
- samFileHeader.getSequenceDictionary().size() +
- ") != number of sequences in binary header (" + sequenceCount + ") for file " + source);
+ throw new SAMFormatException("Number of sequences in text header ("
+ + samFileHeader.getSequenceDictionary().size()
+ + ") != number of sequences in binary header ("
+ + sequenceCount + ") for file " + source);
}
for (int i = 0; i < sequenceCount; i++) {
final SAMSequenceRecord binarySequenceRecord = readSequenceRecord(stream, source);
final SAMSequenceRecord sequenceRecord = samFileHeader.getSequence(i);
if (!sequenceRecord.getSequenceName().equals(binarySequenceRecord.getSequenceName())) {
- throw new SAMFormatException("For sequence " + i + ", text and binary have different names in file " +
- source);
+ throw new SAMFormatException(
+ "For sequence " + i + ", text and binary have different names in file " + source);
}
if (sequenceRecord.getSequenceLength() != binarySequenceRecord.getSequenceLength()) {
- throw new SAMFormatException("For sequence " + i + ", text and binary have different lengths in file " +
- source);
+ throw new SAMFormatException(
+ "For sequence " + i + ", text and binary have different lengths in file " + source);
}
}
} else {
@@ -794,7 +871,6 @@ protected void assertOpen() {
public void remove() {
throw new UnsupportedOperationException("Not supported: remove");
}
-
}
private class EmptyBamIterator extends AbstractBamIterator {
@@ -810,8 +886,8 @@ public SAMRecord next() {
}
/**
-
- /**
+ *
+ * /**
* Iterator for non-indexed sequential iteration through all SAMRecords in file.
* Starting point of iteration is wherever current file position is when the iterator is constructed.
*/
@@ -829,8 +905,8 @@ private class BAMFileIterator extends AbstractBamIterator {
*/
BAMFileIterator(final boolean advance) {
this.bamRecordCodec = new BAMRecordCodec(getFileHeader(), samRecordFactory);
- this.bamRecordCodec.setInputStream(BAMFileReader.this.mStream.getInputStream(),
- BAMFileReader.this.mStream.getInputFileName());
+ this.bamRecordCodec.setInputStream(
+ BAMFileReader.this.mStream.getInputStream(), BAMFileReader.this.mStream.getInputFileName());
if (advance) {
advance();
@@ -861,9 +937,10 @@ void advance() {
mNextRecord.setValidationStringency(mValidationStringency);
if (mValidationStringency != ValidationStringency.SILENT) {
- final List validationErrors = mNextRecord.isValid(mValidationStringency == ValidationStringency.STRICT);
- SAMUtils.processValidationErrors(validationErrors,
- this.samRecordIndex, BAMFileReader.this.getValidationStringency());
+ final List validationErrors =
+ mNextRecord.isValid(mValidationStringency == ValidationStringency.STRICT);
+ SAMUtils.processValidationErrors(
+ validationErrors, this.samRecordIndex, BAMFileReader.this.getValidationStringency());
}
}
if (eagerDecode && mNextRecord != null) {
@@ -882,8 +959,9 @@ SAMRecord getNextRecord() throws IOException {
final SAMRecord next = bamRecordCodec.decode();
final long stopCoordinate = mCompressedInputStream.getFilePointer();
- if(mReader != null && next != null)
- next.setFileSource(new SAMFileSource(mReader,new BAMFileSpan(new Chunk(startCoordinate,stopCoordinate))));
+ if (mReader != null && next != null)
+ next.setFileSource(
+ new SAMFileSource(mReader, new BAMFileSpan(new Chunk(startCoordinate, stopCoordinate))));
return next;
}
@@ -901,8 +979,7 @@ protected SAMRecord peek() {
* @param referenceIndex Desired reference sequence.
* @param start 1-based alignment start.
*/
- private CloseableIterator createStartingAtIndexIterator(final int referenceIndex,
- final int start) {
+ private CloseableIterator createStartingAtIndexIterator(final int referenceIndex, final int start) {
// Hit the index to determine the chunk boundaries for the required data.
final BAMIndex fileIndex = getIndex();
@@ -914,7 +991,7 @@ private CloseableIterator createStartingAtIndexIterator(final int ref
// Add some preprocessing filters for edge-case reads that don't fit into this
// query type.
- return new BAMQueryFilteringIterator(iterator,new BAMStartingAtIteratorFilter(referenceIndex,start));
+ return new BAMQueryFilteringIterator(iterator, new BAMStartingAtIteratorFilter(referenceIndex, start));
}
/**
@@ -927,7 +1004,8 @@ public static BAMFileSpan getFileSpan(QueryInterval[] intervals, BAMIndex fileIn
final BAMFileSpan[] inputSpans = new BAMFileSpan[intervals.length];
for (int i = 0; i < intervals.length; ++i) {
final QueryInterval interval = intervals[i];
- final BAMFileSpan span = fileIndex.getSpanOverlapping(interval.referenceIndex, interval.start, interval.end);
+ final BAMFileSpan span =
+ fileIndex.getSpanOverlapping(interval.referenceIndex, interval.start, interval.end);
inputSpans[i] = span;
}
final BAMFileSpan span;
@@ -939,8 +1017,7 @@ public static BAMFileSpan getFileSpan(QueryInterval[] intervals, BAMIndex fileIn
return span;
}
- private CloseableIterator createIndexIterator(final QueryInterval[] intervals,
- final boolean contained) {
+ private CloseableIterator createIndexIterator(final QueryInterval[] intervals, final boolean contained) {
QueryInterval.assertIntervalsOptimized(intervals);
@@ -951,7 +1028,8 @@ private CloseableIterator createIndexIterator(final QueryInterval[] i
// Add some preprocessing filters for edge-case reads that don't fit into this
// query type.
- return new BAMQueryFilteringIterator(iterator, new BAMQueryMultipleIntervalsIteratorFilter(intervals, contained));
+ return new BAMQueryFilteringIterator(
+ iterator, new BAMQueryMultipleIntervalsIteratorFilter(intervals, contained));
}
/**
@@ -962,9 +1040,8 @@ private CloseableIterator createIndexIterator(final QueryInterval[] i
* @param filePointers file pointer pairs corresponding to chunk boundaries for the
* intervals
*/
- public CloseableIterator createIndexIterator(final QueryInterval[] intervals,
- final boolean contained,
- final long[] filePointers) {
+ public CloseableIterator createIndexIterator(
+ final QueryInterval[] intervals, final boolean contained, final long[] filePointers) {
QueryInterval.assertIntervalsOptimized(intervals);
@@ -973,7 +1050,8 @@ public CloseableIterator