diff --git a/src/main/java/org/broadinstitute/hellbender/tools/CreateBundle.java b/src/main/java/org/broadinstitute/hellbender/tools/CreateBundle.java
index 520e32d764a..8c2567c3309 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/CreateBundle.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/CreateBundle.java
@@ -27,9 +27,9 @@
* and it's associated index file, or a .fasta reference file and it's associated index and dictionary files).
* Bundle files can be supplied as inputs for many GATK tools. The primary advantage to using a bundle input
* over an individual file input is that a bundle allows the individual resources to be located in different
- * directories (ie., when providing a VCF input, it's corresponding index file generally need to be a sibling
- * file in the same directory as the VCF, whereas using a bundle file, because you reference each resource
- * explicitly, the index can be located in a different directory from the VCF).
+ * directories (ie., when providing a VCF input, the corresponding index file generally needs to be a sibling
+ * file in the same directory as the VCF, whereas using a bundle file, because each resource is specified
+ * explicitly, the index file can be located in a different directory than the VCF).
*
* Each resource in a bundle has an associated content type, which is a string that identifies the type of data
* in that resource. One resource in the bundle is always designated as the "primary" resource, which determines
@@ -57,19 +57,19 @@
* may also be supplied.
*
* The simplest way to use CreateBundle is to specify only the primary resource. In this case, with no secondary
- * resources are explicitly provided, CreateBundle will attempt to locate and infer "standard" secondary resources
+ * resources are explicitly provided, CreateBundle will attempt to locate and resolve "standard" secondary resources
* (see "Standard Secondary Resources" below) for the primary resource, as long as:
*
* - the content type of the primary resource can be determined from the resources's file extension
* - the primary resource content type is a well known type (i.e., a variants or a fasta file)
* - the secondary resources are siblings (in the same parent directory) as the primary resource
*
- * The "--suppress-resource-resolution" argument can be used to suppress this secondary
- * resource inference behavior. If the type of the primary resource is not expliclty provided, or cannot be
- * determined from the file extensions, or if the standard secondary resources for a standard primary resource
- * cannot be found in the same director as the primary, an exception will be thrown.
+ * The "--suppress-resource-resolution" argument can be used to suppress secondary resource resolution behavior.
+ * If the type of the primary resource is not explicitly provided, or cannot be determined from the file extension,
+ * or if a standard secondary resource for a standard primary resource cannot be found in the same directory as
+ * the primary, an exception will be thrown.
*
- * Alternatively, you can explicitly specify all of the resources and their content types. This is useful when
+ * Alternatively, you can specify all of the resources and their content types explicitly. This is useful when
* the resources are not in the same directory, or when the content types are not standard.
*
* For the primary resource, if the content type is not specified on the command line (content types are
@@ -82,7 +82,7 @@
*
Standard Content Types
* In general, bundle content types can be any string, but many tools expect bundles to use standard, well known
* content types that are pre-defined, such as content types for a VCF, a VCF index, a .fasta file, or a reference
- * dictionary file. The common well known content types are:
+ * dictionary file. The common well known content type strings that can be used as command line argument tags are:
* Standard VCF Content Types:
*
* - "CT_VARIANT_CONTEXTS": a VCF file
@@ -208,7 +208,7 @@ public class CreateBundle extends CommandLineProgram {
shortName = StandardArgumentDefinitions.SECONDARY_RESOURCE_SHORT_NAME,
doc = "Path to a secondary resource for" + StandardArgumentDefinitions.PRIMARY_RESOURCE_LONG_NAME +
" (usually an index). If no secondary resource is specified, standard secondary resources" +
- " for the primary bundle resource will be automatically inferred unless " +
+ " for the primary bundle resource will be automatically resolved unless " +
SUPPRESS_SECONDARY_RESOURCE_RESOLUTION_FULL_NAME +
" is specified.",
optional = true)
@@ -319,7 +319,7 @@ private Bundle createVCFBundle() {
if (indexPath.isEmpty()) {
throw new IllegalArgumentException(
String.format(
- "Could not infer an index for %s, you must either specify the index path as a secondary input on the command line or specify the %s argument.",
+ "Could not resolve an index for %s, you must either specify the index path as a secondary input on the command line or specify the %s argument.",
primaryResource.getRawInputString(),
SUPPRESS_SECONDARY_RESOURCE_RESOLUTION_FULL_NAME));
}
@@ -344,7 +344,7 @@ private Bundle createVCFBundle() {
private Bundle createHaploidReferenceBundle() {
final Collection bundleResources = new ArrayList<>();
if (secondaryResource == null && (otherResources == null || otherResources.isEmpty())) {
- // infer dictionary and index
+ // resolve dictionary and index
return HaploidReferenceResolver.referenceBundleFromFastaPath(primaryResource, GATKPath::new);
}