make default subject(_id) instead of subject_name/subject_type

subject_name and subject_type are inferred via the subject so we should
make a default subject not default subject_name or subject_type.
reformat/whitespace
remove unused reference_sequence_build
pair model/build
whitespace
remove unused sample creation
convert to Genome::Test::Factory
Add missing include for make_path used in sub create_directory.
whitespace
remove unused test_sample
convert to Genome::Test::Factory
remove unused add_ok
add subset_name so instrument data are valid objects
use test factory so instrument data is a valid object
add cell_type to sample so it is a valid object
Hard trim CHORI ditag reads at 50 bp
Increase temp space requirement for merge sx results
ClinSeq - Add option to update-analysis to allow skipping of archive checks