More review comments.

src/main/java/htsjdk/beta/io/bundle/BundleResourceType.java

@@ -5,8 +5,7 @@
 import htsjdk.beta.plugin.variants.VariantsFormats;
 
 /**
- * Constants for specifying tandard primary content types, secondary content types, and (optional) formats
- * for resources contained in a {@link Bundle}.
+ * Constants for specifying standard content types and formats for resources contained in a {@link Bundle}.
  *
  * Bundles generally contain one primary resource, plus one or more secondary resources such as an index or md5 file.
  * Each resource has an associated content type, and optionally a format. The bundle itself has a primary content
@@ -17,8 +16,8 @@
  * correspond to one of the enum values in {@link htsjdk.beta.plugin.HtsContentType}, since each of these has a
  * corresponding {@link htsjdk.beta.plugin.HtsCodec} that handles that type of resource, such as reads or variants.
  *
- * Secondary resources can also be any string, but the standard secondary content types are defined here, i.e., for
- * primary content type "READS", a secondary content type might be "READS_INDEX".
+ * Secondary resource content types can also be any string, but the standard secondary content types are defined
+ * here, i.e., for primary content type "READS", a secondary content type might be "READS_INDEX".
  *
  * Finally, each resource in a bundle can have an optional format, which is a string that corresponds to the format
  * for that resource. For example, a primary content type of "READS" might have a format of "BAM".

src/main/java/htsjdk/beta/plugin/reads/ReadsBundle.java

@@ -47,9 +47,7 @@ public class ReadsBundle<T extends IOPath> extends Bundle implements Serializabl
  * @param reads An {@link IOPath}-derived object that represents a source of reads.
  */
  public ReadsBundle(final T reads) {
- this(Arrays.asList(toInputResource(
- BundleResourceType.CT_ALIGNED_READS,
- ValidationUtils.nonNull(reads, BundleResourceType.CT_ALIGNED_READS))));
+ this(Arrays.asList(toInputResource(BundleResourceType.CT_ALIGNED_READS, reads)));
  }
 
  /**
@@ -59,10 +57,8 @@ public ReadsBundle(final T reads) {
  */
  public ReadsBundle(final T reads, final T index) {
  this(Arrays.asList(
- toInputResource(BundleResourceType.CT_ALIGNED_READS, ValidationUtils.nonNull(reads, BundleResourceType.CT_ALIGNED_READS)),
- toInputResource(
- BundleResourceType.CT_READS_INDEX,
- ValidationUtils.nonNull(index, BundleResourceType.CT_READS_INDEX))));
+ toInputResource(BundleResourceType.CT_ALIGNED_READS, reads),
+ toInputResource(BundleResourceType.CT_READS_INDEX, index)));
  }
 
  /**
@@ -174,10 +170,6 @@ public static <T extends IOPath> ReadsBundle<T> resolveIndex(
  return new ReadsBundle<>(reads);
  }
 
- public static boolean looksLikeAReadsBundle(final IOPath rawReadPath) {
- return rawReadPath.getURI().getPath().endsWith(BundleJSON.BUNDLE_EXTENSION);
- }
-
  private static <T extends IOPath> IOPathResource toInputResource(final String providedContentType, final T ioPath) {
  ValidationUtils.nonNull(ioPath, "ioPath");
  final Optional<Tuple<String, String>> typePair = getInferredContentTypes(ioPath);