write legend file with id mapping to read group information
Add accessors for tags on profile items.
Correct "use" to use the module we're really using.
New command to assign tags to configuration items.
New command to remove tags from configuration items.
Remove deprecated ccs-vcf for indels

Users should use the newer version of this command at:

gmt vcf cross-sample indel
Use cmp_bag instead of worrying about sorting in tests.
Make it possible to disable summarization.

The documentation claims a negative value could be used to disable
summarization. This makes it true.
Make --summary-threshold 0 always summarize.
added trv_type_category to the vep interpreter
Merge branch 'master' of https://github.com/genome/genome into lumpy
find correct read group more efficiently
fixed typo
remove 'genome model reference-sequence generate-bitmask'

This command calls reallocate on
Genome::Model::Build::ImportedReferenceSequence which it cannot due so
this command, if used, would crash.  There does not seem to be a record
of its usage in the usage_log.

CHANGELOG: Remove 'genome model reference-sequence generate-bitmask',
which appears to be unused and broken.
cleaned up formatting
add read_group_info to the output
use G::M::T::Sam::ListReadGroups
use Genome::File::Tsv to write legend file
make splice_sites and non_synonymous lists a state variable
update default clin-seq pp