write legend file with id mapping to read group information
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
Remove unused 'completed' allocation status
make splice_sites and non_synonymous lists a state variable
change query_tcga_barcode timeout, sleep, and attempts

Previous, default timeout was 180s, sleep was 60s, and attempts was 5.
This mean query_tcga_barcode would hang for 20 minutes is the TCGA UUID
Browser was down.  Instrumentation so far shows that so far it has always
either succeeded on the first attempt or failed and that the upper bound
on average successful response times was 700 ms.

Now the default timeout is 5s (much greater than 700ms), sleep is 10s,
and attempts is 8 which means query_tcga_barcode will hang for 2 minutes
if the TCGA UUID Browser is down.

This will prevent tests from failing and should, presumably, not cause
an increase in failure rates (due to the first attempt succeeds or it
fails).  Future instrumentation values will allow us to verify.
Updated class browser cache.
Updated `genome` tab completion.
Rename write_header_to_legend_file to create_legend_writer
Rename extract_id_and_lib_values to extract_id_and_lb_values
Pull extract_id_and_lb_values into the main _detect_variants so that it's only executed once for each bam
state variables can stay inside of their respective subroutines
Merge pull request #19 from nnutter/query_tcga_barcode

change query_tcga_barcode timeout, sleep, and attempts