Respect the max_records_in_ram property by passing along to picard command.  Set re_reverse default to true to match Picard default behaviour.
Add homopolymer indel filter to trio reports.  Use meaningful output file extensions. Update the test data directory with the new output files.
Merge branch 'master' of https://github.com/genome/genome into trio_with_homopolymer
Add the test data
Add bam_readcount_version to somatic-variation pp, use it.

Previously the CreateReport step was just leaning on the default version
of bam-readcount. This will ensure this no longer happens.
Use Test::Factory so we do not fail on new required properties.
Formatting improvements
bam_readcount_version is no longer optional
Add bam_readcount_version and pass it along
Add bam_readcount_version to commands that call AddReadcounts.

Update a whole lote of tests to include a version.
changing instance of patient out for the more generally applicable individual, this may break some analyst scripts that I will attempt to discover
rename genome model instrument-data assign expression for clarity
Clarify help text at Dave Larson's request
add blurb about how to run tests to README
Call Genome::Model::Command::InstrumentData::Assign::Expression by the new name
Relax validation of reporter plan

Allow additional interpreters that aren't "required" by the reporter
Vcf reporter requires only minimal interpreters

We can now specify arbitrary "filterpreters" to be
used with the vcf reporter.  We don't need the specialized
vcf reporters that simply add another "required" interpreter.
making tests pass in PR - Merge branch 'master' into somvar-readcount
Use the microarray input format instead of the name of the processing profile during GenotypeMicroarray model define.
Merge pull request #68 from apregier/relax-vcf-reporter

Relax vcf reporter