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.
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.
admin: fix minor typo
report: fix minor typo
Remove breakpoint from test.
various typo fixes and additions to documentation
further additions to fill in genome model modules with no documentation
various minor improvements to clin-seq and other pipeline documentation
update docs that appear when the user type genome --help
updated ur submodule to 07f8e91
Merge pull request #61 from gsanders/somvar-readcount

Add bam_readcount_version to somatic_variation