Implements collections of bundles. (#1702)

src/main/java/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.java

@@ -32,7 +32,7 @@ public class FASTADecoderV1_0 implements HaploidReferenceDecoder {
     public FASTADecoderV1_0(final Bundle inputBundle) {
         this.inputBundle = inputBundle;
         this.displayName = inputBundle.getPrimaryResource().getDisplayName();
-        final BundleResource referenceResource = inputBundle.getOrThrow(BundleResourceType.HAPLOID_REFERENCE);
+        final BundleResource referenceResource = inputBundle.getOrThrow(BundleResourceType.CT_HAPLOID_REFERENCE);
         if (referenceResource.getIOPath().isPresent()) {
             referenceSequenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(
                     referenceResource.getIOPath().get().toPath(), true);
@@ -129,7 +129,7 @@ public void close() {
      * @return true if input {@link Bundle} contains a reads index resource
      */
     private static boolean bundleContainsIndex(final Bundle inputBundle) {
-        return inputBundle.get(BundleResourceType.READS_INDEX).isPresent();
+        return inputBundle.get(BundleResourceType.CT_READS_INDEX).isPresent();
     }
 
 }

src/main/java/htsjdk/beta/codecs/reads/ReadsCodecUtils.java

@@ -36,11 +36,11 @@ public static SamInputResource bundleToSamInputResource(
             final ReadsDecoderOptions readsDecoderOptions) {
         final SamInputResource samInputResource = readsToSamInputResource(
                 inputBundle,
-                BundleResourceType.ALIGNED_READS,
+                BundleResourceType.CT_ALIGNED_READS,
                 readsDecoderOptions);
         indexToSamInputResource(
                 inputBundle,
-                BundleResourceType.READS_INDEX,
+                BundleResourceType.CT_READS_INDEX,
                 readsDecoderOptions,
                 samInputResource);
         return samInputResource;
@@ -77,7 +77,7 @@ public static void readsDecoderOptionsToSamReaderFactory(
      */
     @InternalAPI
     public static boolean bundleContainsIndex(final Bundle inputBundle) {
-        return inputBundle.get(BundleResourceType.READS_INDEX).isPresent();
+        return inputBundle.get(BundleResourceType.CT_READS_INDEX).isPresent();
     }
 
     /**

src/main/java/htsjdk/beta/codecs/reads/bam/BAMCodec.java

@@ -16,7 +16,7 @@
 /**
  * InternalAPI
  *
- * Base class for {@link BundleResourceType#READS_BAM} codecs.
+ * Base class for {@link BundleResourceType#FMT_READS_BAM} codecs.
  */
 @InternalAPI
 public abstract class BAMCodec implements ReadsCodec {

src/main/java/htsjdk/beta/codecs/reads/bam/BAMDecoder.java

@@ -11,7 +11,7 @@
 /**
  * InternalAPI
  *
- * Base class for {@link BundleResourceType#READS_BAM} decoders.
+ * Base class for {@link BundleResourceType#FMT_READS_BAM} decoders.
  */
 @InternalAPI
 public abstract class BAMDecoder implements ReadsDecoder {
@@ -21,7 +21,7 @@ public abstract class BAMDecoder implements ReadsDecoder {
 
     /**
      * Create a BAM decoder for the given input bundle. The primary resource in the bundle must
-     * have content type {@link BundleResourceType#ALIGNED_READS}, and the resource must be an
+     * have content type {@link BundleResourceType#CT_ALIGNED_READS}, and the resource must be an
      * appropriate format and version for this encoder (to find an encoder for a bundle, see
      * {@link htsjdk.beta.plugin.registry.ReadsResolver}.
      *
@@ -34,7 +34,7 @@ public BAMDecoder(final Bundle inputBundle, final ReadsDecoderOptions readsDecod
         ValidationUtils.nonNull(readsDecoderOptions, "readsDecoderOptions");
 
         this.inputBundle = inputBundle;
-        this.displayName = inputBundle.getOrThrow(BundleResourceType.ALIGNED_READS).getDisplayName();
+        this.displayName = inputBundle.getOrThrow(BundleResourceType.CT_ALIGNED_READS).getDisplayName();
         this.readsDecoderOptions = readsDecoderOptions;
     }
 

src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoder.java

@@ -10,7 +10,7 @@
 /**
  * InternalAPI
  *
- * Base class for {@link BundleResourceType#READS_BAM} encoders.
+ * Base class for {@link BundleResourceType#FMT_READS_BAM} encoders.
  */
 public abstract class BAMEncoder implements ReadsEncoder {
     private final Bundle outputBundle;
@@ -21,7 +21,7 @@ public abstract class BAMEncoder implements ReadsEncoder {
      * InternalAPI
      *
      * Create a BAM encoder for the given output bundle. The primary resource in the bundle must
-     * have content type {@link BundleResourceType#ALIGNED_READS} (to find a decoder for a bundle,
+     * have content type {@link BundleResourceType#CT_ALIGNED_READS} (to find a decoder for a bundle,
      * see {@link htsjdk.beta.plugin.registry.ReadsResolver}).
      *
      * NOTE: callers that provide an output stream resource should provide a buffered output stream
@@ -36,7 +36,7 @@ public BAMEncoder(final Bundle outputBundle, final ReadsEncoderOptions readsEnco
 
         this.outputBundle = outputBundle;
         this.readsEncoderOptions = readsEncoderOptions;
-        this.displayName = outputBundle.getOrThrow(BundleResourceType.ALIGNED_READS).getDisplayName();
+        this.displayName = outputBundle.getOrThrow(BundleResourceType.CT_ALIGNED_READS).getDisplayName();
     }
 
     @Override

src/main/java/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.java

@@ -32,9 +32,9 @@ public class BAMDecoderV1_0 extends BAMDecoder {
 
     /**
      * Create a V1.0 BAM decoder for the given input bundle. The primary resource in the bundle must
-     * have content type {@link BundleResourceType#ALIGNED_READS}, and the resource must be an
+     * have content type {@link BundleResourceType#CT_ALIGNED_READS}, and the resource must be an
      * appropriate format and version for this encoder (to find an encoder for a bundle, see
-     * {@link htsjdk.beta.plugin.registry.ReadsResolver}.
+     * {@link htsjdk.beta.plugin.registry.ReadsResolver}).
      *
      * @param inputBundle bundle to decoder
      * @param readsDecoderOptions options to use

src/main/java/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.java

@@ -24,7 +24,7 @@ public class BAMEncoderV1_0 extends BAMEncoder {
 
     /**
      * Create a V1.0 BAM encoder for the given output bundle. The primary resource in the bundle must
-     * have content type {@link BundleResourceType#ALIGNED_READS} (to find a decoder for a bundle,
+     * have content type {@link BundleResourceType#CT_ALIGNED_READS} (to find a decoder for a bundle,
      * see {@link htsjdk.beta.plugin.registry.ReadsResolver}).
      *
      * @param outputBundle bundle to encode
@@ -87,9 +87,9 @@ private SAMFileWriter getBAMFileWriter(
 
         final boolean preSorted = readsEncoderOptions.isPreSorted();
 
-        final BundleResource readsResource = getOutputBundle().getOrThrow(BundleResourceType.ALIGNED_READS);
-        final Optional<BundleResource> optIndexResource = getOutputBundle().get(BundleResourceType.READS_INDEX);
-        final Optional<BundleResource> optMD5Resource = getOutputBundle().get(BundleResourceType.MD5);
+        final BundleResource readsResource = getOutputBundle().getOrThrow(BundleResourceType.CT_ALIGNED_READS);
+        final Optional<BundleResource> optIndexResource = getOutputBundle().get(BundleResourceType.CT_READS_INDEX);
+        final Optional<BundleResource> optMD5Resource = getOutputBundle().get(BundleResourceType.CT_MD5);
 
         //TODO: BAMFileWriter currently only supports writing an index to a plain file, so for now
         // throw if an index is requested on any other type

src/main/java/htsjdk/beta/codecs/reads/cram/CRAMCodec.java

@@ -26,7 +26,7 @@
 /**
  * InternalAPI
  *
- * Base class for {@link BundleResourceType#READS_CRAM} codecs.
+ * Base class for {@link BundleResourceType#FMT_READS_CRAM} codecs.
  */
 @InternalAPI
 public abstract class CRAMCodec implements ReadsCodec {

src/main/java/htsjdk/beta/codecs/reads/cram/CRAMDecoder.java

@@ -31,7 +31,7 @@
 /**
  * InternalAPI
  *
- * Base class for {@link BundleResourceType#READS_CRAM} decoders.
+ * Base class for {@link BundleResourceType#FMT_READS_CRAM} decoders.
  */
 @InternalAPI
 public abstract class CRAMDecoder implements ReadsDecoder {
@@ -57,7 +57,7 @@ public CRAMDecoder(final Bundle inputBundle, final ReadsDecoderOptions readsDeco
 
         this.inputBundle = inputBundle;
         this.readsDecoderOptions = readsDecoderOptions;
-        this.displayName = inputBundle.getOrThrow(BundleResourceType.ALIGNED_READS).getDisplayName();
+        this.displayName = inputBundle.getOrThrow(BundleResourceType.CT_ALIGNED_READS).getDisplayName();
 
         samReader = getSamReaderForCRAM(inputBundle, readsDecoderOptions);
         samFileHeader = samReader.getFileHeader();

src/main/java/htsjdk/beta/codecs/reads/cram/CRAMEncoder.java

@@ -21,7 +21,7 @@
 /**
  * InternalAPI
  *
- * Base class for {@link BundleResourceType#READS_CRAM} decoders.
+ * Base class for {@link BundleResourceType#FMT_READS_CRAM} decoders.
  */
 @InternalAPI
 public abstract class CRAMEncoder implements ReadsEncoder {
@@ -34,7 +34,7 @@ public abstract class CRAMEncoder implements ReadsEncoder {
      * InternalAPI
      *
      * Create a CRAM encoder for the given output bundle. The primary resource in the bundle must
-     * have content type {@link BundleResourceType#ALIGNED_READS} (to find a decoder for a bundle,
+     * have content type {@link BundleResourceType#CT_ALIGNED_READS} (to find a decoder for a bundle,
      * see {@link htsjdk.beta.plugin.registry.ReadsResolver}).
      *
      * @param outputBundle bundle to encode
@@ -47,7 +47,7 @@ public CRAMEncoder(final Bundle outputBundle, final ReadsEncoderOptions readsEnc
 
         this.outputBundle = outputBundle;
         this.readsEncoderOptions = readsEncoderOptions;
-        this.displayName = outputBundle.getOrThrow(BundleResourceType.ALIGNED_READS).getDisplayName();
+        this.displayName = outputBundle.getOrThrow(BundleResourceType.CT_ALIGNED_READS).getDisplayName();
     }
 
     @Override
@@ -128,7 +128,7 @@ private CRAMFileWriter getCRAMWriter(final SAMFileHeader samFileHeader, final Re
         // the CRAMFileWriter constructors assume presorted; so if we're presorted, use the CRAMFileWriters
         // directly so we can support writing to a stream
         if (readsEncoderOptions.isPreSorted()) {
-            final BundleResource outputResource = outputBundle.getOrThrow(BundleResourceType.ALIGNED_READS);
+            final BundleResource outputResource = outputBundle.getOrThrow(BundleResourceType.CT_ALIGNED_READS);
             if (outputResource.getIOPath().isPresent()) {
                 cramFileWriter = new CRAMFileWriter(
                         outputResource.getIOPath().get().getOutputStream(),
@@ -149,9 +149,9 @@ private CRAMFileWriter getCRAMWriter(final SAMFileHeader samFileHeader, final Re
             final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
             final boolean preSorted = readsEncoderOptions.isPreSorted();
 
-            final BundleResource readsResource = getOutputBundle().getOrThrow(BundleResourceType.ALIGNED_READS);
-            final Optional<BundleResource> optIndexResource = getOutputBundle().get(BundleResourceType.READS_INDEX);
-            final Optional<BundleResource> optMD5Resource = getOutputBundle().get(BundleResourceType.MD5);
+            final BundleResource readsResource = getOutputBundle().getOrThrow(BundleResourceType.CT_ALIGNED_READS);
+            final Optional<BundleResource> optIndexResource = getOutputBundle().get(BundleResourceType.CT_READS_INDEX);
+            final Optional<BundleResource> optMD5Resource = getOutputBundle().get(BundleResourceType.CT_MD5);
 
             //TODO: SamFileWriterFactory code paths currently only support writing an index to a plain file, so
             // for now throw if an index is requested on any other type

src/main/java/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMDecoderV2_1.java

@@ -13,7 +13,7 @@ public class CRAMDecoderV2_1 extends CRAMDecoder {
 
     /**
      * Create a new V2.1 CRAM decoder. The primary resource in the input
-     * bundle must have content type {@link BundleResourceType#ALIGNED_READS} (to find a decoder for a bundle,
+     * bundle must have content type {@link BundleResourceType#CT_ALIGNED_READS} (to find a decoder for a bundle,
      * see {@link htsjdk.beta.plugin.registry.ReadsResolver}).
      *
      * @param bundle the input {@link Bundle} to decode

src/main/java/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMEncoderV2_1.java

@@ -13,7 +13,7 @@ public class CRAMEncoderV2_1 extends CRAMEncoder {
 
     /**
      * Create a CRAM encoder for the given output bundle. The primary resource in the bundle must
-     * have content type {@link BundleResourceType#ALIGNED_READS} (to find a decoder for a bundle,
+     * have content type {@link BundleResourceType#CT_ALIGNED_READS} (to find a decoder for a bundle,
      * see {@link htsjdk.beta.plugin.registry.ReadsResolver}).
      *
      * @param outputBundle bundle to encode

src/main/java/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMDecoderV3_0.java

@@ -13,7 +13,7 @@ public class CRAMDecoderV3_0 extends CRAMDecoder {
 
     /**
      * Create a new CRAM V3.0 decoder. The primary resource in the input
-     * bundle must have content type {@link BundleResourceType#ALIGNED_READS} (to find a decoder for a bundle,
+     * bundle must have content type {@link BundleResourceType#CT_ALIGNED_READS} (to find a decoder for a bundle,
      * see {@link htsjdk.beta.plugin.registry.ReadsResolver}).
      *
      * @param bundle input {@link Bundle} to decode

src/main/java/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMEncoderV3_0.java

@@ -13,7 +13,7 @@ public class CRAMEncoderV3_0 extends CRAMEncoder {
 
     /**
      * Create a new CRAM CRAM v3.0 encoder for the given output bundle. The primary resource in the
-     * bundle must have content type {@link BundleResourceType#ALIGNED_READS} (to find an encoder for a bundle,
+     * bundle must have content type {@link BundleResourceType#CT_ALIGNED_READS} (to find an encoder for a bundle,
      * see {@link htsjdk.beta.plugin.registry.ReadsResolver}).
      *
      * @param outputBundle output {@link Bundle} to encode

src/main/java/htsjdk/beta/codecs/reads/htsget/HtsgetBAMCodec.java

@@ -18,7 +18,7 @@
 
 /**
  * Base class for concrete implementations of reads codecs that handle
- * {@link BundleResourceType#READS_HTSGET_BAM} codecs.
+ * {@link BundleResourceType#FMT_READS_HTSGET_BAM} codecs.
  *
  * Note: writing to htsget is not supported, so there is no Htsget encoder.
  */

src/main/java/htsjdk/beta/codecs/reads/htsget/HtsgetBAMDecoder.java

@@ -9,7 +9,7 @@
 
 /**
  * Base class for concrete implementations of reads decoders that handle
- * {@link BundleResourceType#READS_HTSGET_BAM} decoding.
+ * {@link BundleResourceType#FMT_READS_HTSGET_BAM} decoding.
  */
 public abstract class HtsgetBAMDecoder implements ReadsDecoder {
     private final Bundle inputBundle;
@@ -19,7 +19,7 @@ public abstract class HtsgetBAMDecoder implements ReadsDecoder {
     public HtsgetBAMDecoder(final Bundle inputBundle, final ReadsDecoderOptions readsDecoderOptions) {
         this.inputBundle = inputBundle;
         this.readsDecoderOptions = readsDecoderOptions;
-        this.displayName = inputBundle.getOrThrow(BundleResourceType.ALIGNED_READS).getDisplayName();
+        this.displayName = inputBundle.getOrThrow(BundleResourceType.CT_ALIGNED_READS).getDisplayName();
     }
 
     @Override

src/main/java/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMCodecV1_2.java

@@ -14,14 +14,14 @@
 import java.util.Optional;
 
 /**
- * Version 1.2 of {@link BundleResourceType#READS_HTSGET_BAM} codec.
+ * Version 1.2 of {@link BundleResourceType#FMT_READS_HTSGET_BAM} codec.
  */
 public class HtsgetBAMCodecV1_2 extends HtsgetBAMCodec {
 
     @Override
     public HtsgetBAMDecoder getDecoder(final Bundle inputBundle,
                                        final ReadsDecoderOptions decodeOptions) {
-        final BundleResource readsResource = inputBundle.getOrThrow(BundleResourceType.ALIGNED_READS);
+        final BundleResource readsResource = inputBundle.getOrThrow(BundleResourceType.CT_ALIGNED_READS);
         final Optional<IOPath> inputPath = readsResource.getIOPath();
         if (!inputPath.isPresent()) {
             throw new IllegalArgumentException("The reads source must be a IOPath");

src/main/java/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMDecoderV1_2.java

@@ -22,15 +22,15 @@
 import java.util.Optional;
 
 /**
- * Version 1.2 of {@link BundleResourceType#READS_HTSGET_BAM} decoder.
+ * Version 1.2 of {@link BundleResourceType#FMT_READS_HTSGET_BAM} decoder.
  */
 public class HtsgetBAMDecoderV1_2 extends HtsgetBAMDecoder {
 
     final HtsgetBAMFileReader htsgetReader;
 
     public HtsgetBAMDecoderV1_2(final Bundle inputBundle, final ReadsDecoderOptions decoderOptions) {
         super(inputBundle, decoderOptions);
-        final BundleResource readsResource = inputBundle.getOrThrow(BundleResourceType.ALIGNED_READS);
+        final BundleResource readsResource = inputBundle.getOrThrow(BundleResourceType.CT_ALIGNED_READS);
         if (!readsResource.getIOPath().isPresent()) {
             throw new IllegalArgumentException(String.format(
                     "Htsget requires an IOPath input resource. The bundle resource %s doesn't contain the required IOPath.",

src/main/java/htsjdk/beta/codecs/reads/sam/SAMCodec.java

@@ -15,7 +15,7 @@
 /**
  * InternalAPI
  *
- * Base class for {@link BundleResourceType#READS_SAM} codecs.
+ * Base class for {@link BundleResourceType#FMT_READS_SAM} codecs.
  */
 @InternalAPI
 public abstract class SAMCodec implements ReadsCodec {

src/main/java/htsjdk/beta/codecs/reads/sam/SAMDecoder.java

@@ -11,7 +11,7 @@
 /**
  * InternalAPI
  *
- * Base class for {@link BundleResourceType#READS_SAM} decoders.
+ * Base class for {@link BundleResourceType#FMT_READS_SAM} decoders.
  */
 @InternalAPI
 public abstract class SAMDecoder implements ReadsDecoder {
@@ -21,7 +21,7 @@ public abstract class SAMDecoder implements ReadsDecoder {
 
     /**
      * Create a SAM decoder for the given input bundle. The primary resource in the bundle must
-     * have content type {@link BundleResourceType#ALIGNED_READS}, and the resource must be an
+     * have content type {@link BundleResourceType#CT_ALIGNED_READS}, and the resource must be an
      * appropriate format and version for this encoder (to find an encoder for a bundle, see
      * {@link htsjdk.beta.plugin.registry.ReadsResolver}.
      *
@@ -33,7 +33,7 @@ public SAMDecoder(final Bundle inputBundle, final ReadsDecoderOptions readsDecod
         ValidationUtils.nonNull(inputBundle,"inputBundle");
         ValidationUtils.nonNull(readsDecoderOptions, "readsDecoderOptions");
         this.inputBundle = inputBundle;
-        this.displayName = inputBundle.getOrThrow(BundleResourceType.ALIGNED_READS).getDisplayName();
+        this.displayName = inputBundle.getOrThrow(BundleResourceType.CT_ALIGNED_READS).getDisplayName();
         this.readsDecoderOptions = readsDecoderOptions;
     }
 

src/main/java/htsjdk/beta/codecs/reads/sam/SAMEncoder.java

@@ -9,7 +9,7 @@
 /**
  * InternalAPI
  *
- * Base class for {@link BundleResourceType#READS_SAM} encoders.
+ * Base class for {@link BundleResourceType#FMT_READS_SAM} encoders.
  */
 public abstract class SAMEncoder implements ReadsEncoder {
     private final Bundle outputBundle;
@@ -20,7 +20,7 @@ public abstract class SAMEncoder implements ReadsEncoder {
      * InternalAPI
      *
      * Create a SAM encoder for the given output bundle. The primary resource in the bundle must
-     * have content type {@link BundleResourceType#ALIGNED_READS} (to find a decoder for a bundle,
+     * have content type {@link BundleResourceType#CT_ALIGNED_READS} (to find a decoder for a bundle,
      * see {@link htsjdk.beta.plugin.registry.ReadsResolver}).
      *
      * NOTE: callers that provide an output stream resource should provide a buffered output stream
@@ -32,7 +32,7 @@ public abstract class SAMEncoder implements ReadsEncoder {
     public SAMEncoder(final Bundle outputBundle, final ReadsEncoderOptions readsEncoderOptions) {
         this.outputBundle = outputBundle;
         this.readsEncoderOptions = readsEncoderOptions;
-        this.displayName = outputBundle.getOrThrow(BundleResourceType.ALIGNED_READS).getDisplayName();
+        this.displayName = outputBundle.getOrThrow(BundleResourceType.CT_ALIGNED_READS).getDisplayName();
     }
 
     @Override

src/main/java/htsjdk/beta/codecs/reads/sam/samV1_0/SAMDecoderV1_0.java

@@ -25,7 +25,7 @@ public class SAMDecoderV1_0 extends SAMDecoder {
 
     /**
      * Create a V1.0 SAM decoder for the given input bundle. The primary resource in the bundle must
-     * have content type {@link BundleResourceType#ALIGNED_READS}, and the resource must be an
+     * have content type {@link BundleResourceType#CT_ALIGNED_READS}, and the resource must be an
      * appropriate format and version for this encoder (to find an encoder for a bundle, see
      * {@link htsjdk.beta.plugin.registry.ReadsResolver}.
      *