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 "--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:

*