htsjdk.beta.plugin.registry.VariantsResolver Maven / Gradle / Ivy
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package htsjdk.beta.plugin.registry;
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.variants.VariantsCodec;
import htsjdk.beta.plugin.variants.VariantsDecoder;
import htsjdk.beta.plugin.variants.VariantsDecoderOptions;
import htsjdk.beta.plugin.variants.VariantsEncoder;
import htsjdk.beta.plugin.variants.VariantsEncoderOptions;
import htsjdk.io.IOPath;
import htsjdk.utils.ValidationUtils;
/**
* Class with methods for resolving inputs and outputs to variants encoders and decoders.
*
* Provides a convenient typesafe layer over the {@link HtsCodecResolver} used by an
* {@link HtsCodecRegistry} to manage {@link VariantsCodec}s
* (see {@link HtsCodecRegistry#getHaploidReferenceResolver()}).
*
* Provides typesafe conversion of argument and return types to types that conform to those
* used with {@link VariantsCodec}s, such as {@link VariantsDecoder}, {@link VariantsEncoder},
* {@link htsjdk.beta.plugin.variants.VariantsDecoderOptions}.
*/
public class VariantsResolver extends HtsCodecResolver {
/**
* Create a VariantsResolver.
*/
public VariantsResolver() {
super(BundleResourceType.VARIANT_CONTEXTS);
}
/**
* Get a {@link VariantsDecoder} suitable for decoding {@code inputPath}.
*
* @param inputPath the input path to decode
* @return a {@link VariantsDecoder} suitable for decoding {@code inputPath}
* @throws HtsjdkException if no registered codecs can handle the resource
* @throws HtsjdkPluginException if more than one codec claims to handle the resource. this usually indicates
* that the registry contains an incorrectly written codec.
*/
public VariantsDecoder getVariantsDecoder(final IOPath inputPath) {
ValidationUtils.nonNull(inputPath, "Input path");
return getVariantsDecoder(inputPath, new VariantsDecoderOptions());
}
/**
* Get a {@link VariantsDecoder} suitable for decoding {@code inputPath} using {@code variantsDecoderOptions}.
*
* @param inputPath the input path to decode
* @param variantsDecoderOptions decoder options to use
* @return a {@link VariantsDecoder} suitable for decoding {@code inputPath}
* @throws HtsjdkException if no registered codecs can handle the resource
* @throws HtsjdkPluginException if more than one codec claims to handle the resource. this usually indicates
* that the registry contains an incorrectly written codec.
*/
public VariantsDecoder getVariantsDecoder(
final IOPath inputPath,
final VariantsDecoderOptions variantsDecoderOptions) {
ValidationUtils.nonNull(inputPath, "Input path");
ValidationUtils.nonNull(variantsDecoderOptions, "Decoder options");
final Bundle inputBundle = new BundleBuilder()
.addPrimary(new IOPathResource(inputPath, BundleResourceType.VARIANT_CONTEXTS))
.build();
return getVariantsDecoder(inputBundle, variantsDecoderOptions);
}
/**
* Get a {@link VariantsDecoder} suitable for decoding {@code inputBundle}.
*
* @param inputBundle the input bundle containing resources to decode
* @return a {@link VariantsDecoder} suitable for decoding {@code inputBundle}
* @throws HtsjdkException if no registered codecs can handle the resource
* @throws HtsjdkPluginException if more than one codec claims to handle the resource. this usually indicates
* that the registry contains an incorrectly written codec.
*/
@SuppressWarnings("unchecked")
public VariantsDecoder getVariantsDecoder(final Bundle inputBundle) {
ValidationUtils.nonNull(inputBundle, "Input bundle");
final VariantsCodec variantsCodec = resolveForDecoding(inputBundle);
return (VariantsDecoder) variantsCodec.getDecoder(inputBundle, new VariantsDecoderOptions());
}
/**
* Get a {@link VariantsDecoder} suitable for decoding {@code inputBundle} using {@code variantsDecoderOptions}.
*
* @param inputBundle the input bundle to decode
* @param variantsDecoderOptions decoder options to use
* @return a {@link VariantsDecoder} suitable for decoding {@code inputBundle}
* @throws HtsjdkException if no registered codecs can handle the resource
* @throws HtsjdkPluginException if more than one codec claims to handle the resource. this usually indicates
* that the registry contains an incorrectly written codec.
*/
@SuppressWarnings("unchecked")
public VariantsDecoder getVariantsDecoder(
final Bundle inputBundle,
final VariantsDecoderOptions variantsDecoderOptions) {
ValidationUtils.nonNull(inputBundle, "Input bundle");
ValidationUtils.nonNull(variantsDecoderOptions, "Decoder options");
final VariantsCodec variantsCodec = resolveForDecoding(inputBundle);
return (VariantsDecoder) variantsCodec.getDecoder(inputBundle, variantsDecoderOptions);
}
/**
* Get a {@link VariantsEncoder} suitable for encoding to {@code outputPath}.
*
* @param outputPath path to encode to
* @return a {@link VariantsEncoder} suitable for encoding to {@code outputPath}
* @throws HtsjdkException if no registered codecs can handle the resource
* @throws HtsjdkPluginException if more than one codec claims to handle the resource. this usually indicates
* that the registry contains an incorrectly written codec.
*/
public VariantsEncoder getVariantsEncoder(final IOPath outputPath) {
ValidationUtils.nonNull(outputPath, "Output path");
return getVariantsEncoder(outputPath, new VariantsEncoderOptions());
}
/**
* Get a {@link VariantsEncoder} suitable for encoding to {@code outputPath} using {@code variantsEncoderOptions}.
*
* @param outputPath path to encode to
* @param variantsEncoderOptions encoder options to use
* @return a {@link VariantsEncoder} suitable for encoding to {@code outputPath}
* @throws HtsjdkException if no registered codecs can handle the resource
* @throws HtsjdkPluginException if more than one codec claims to handle the resource. this usually indicates
* that the registry contains an incorrectly written codec.
*/
public VariantsEncoder getVariantsEncoder(
final IOPath outputPath,
final VariantsEncoderOptions variantsEncoderOptions) {
ValidationUtils.nonNull(outputPath, "Output path");
ValidationUtils.nonNull(variantsEncoderOptions, "Encoder options");
final Bundle outputBundle = new BundleBuilder()
.addPrimary(new IOPathResource(outputPath, BundleResourceType.VARIANT_CONTEXTS))
.build();
return getVariantsEncoder(outputBundle, variantsEncoderOptions);
}
/**
* Get a {@link VariantsEncoder} suitable for encoding to {@code outputBundle} using {@code variantsEncoderOptions}.
*
* @param outputBundle output bundle containg resources to encode to
* @param variantsEncoderOptions options to use
* @return a {@link VariantsEncoder} suitable for encoding to {@code outputBundle}
* @throws HtsjdkException if no registered codecs can handle the resource
* @throws HtsjdkPluginException if more than one codec claims to handle the resource. this usually indicates
* that the registry contains an incorrectly written codec.
*/
public VariantsEncoder getVariantsEncoder(
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
// 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);
}
/**
* Get a {@link VariantsEncoder} suitable for encoding to {@code outputBundle} using
* {@code variantsEncoderOptions}, specifying a version and output format.
*
* @param outputBundle output bundle containing resources to encode to
* @param variantsEncoderOptions options to use
* @param variantsFormat the output format to use
* @param formatVersion the format version to use
* @return a {@link VariantsEncoder} suitable for encoding to {@code outputBundle}
* @throws HtsjdkException if no registered codecs can handle the resource
* @throws HtsjdkPluginException if more than one codec claims to handle the resource. this usually indicates
* that the registry contains an incorrectly written codec.
*/
@SuppressWarnings("unchecked")
public VariantsEncoder getVariantsEncoder(
final Bundle outputBundle,
final VariantsEncoderOptions variantsEncoderOptions,
final String variantsFormat,
final HtsVersion formatVersion) {
ValidationUtils.nonNull(outputBundle, "Output bundle");
ValidationUtils.nonNull(variantsEncoderOptions, "Encoder options");
ValidationUtils.nonNull(variantsFormat, "Format");
ValidationUtils.nonNull(formatVersion, "Format version");
return (VariantsEncoder) resolveFormatAndVersion(variantsFormat, formatVersion)
.getEncoder(outputBundle, variantsEncoderOptions);
}
}