Initial revision of an ERCC spike-in QC command.  This needs to be in a pipeline with software results.
A new version of the ERCC spike-in QC that uses existing RNA-seq alignments to a reference and annotation that includes the ERCC transcripts.
Epitope Prediction : New Module Added
Merge branch 'master' of github.com:genome/genome
Merge branch 'master' of github.com:genome/genome
Epitope prediction : Changes to BindingFilter.pm per feedback on pull request
Use last_succeeded_build instead of lastest_build
Epitope Prediction : Removed referencesto references in BindingFilter.pm
Set ALTERNATE_FROM_CLASS in command-line entry points.
Stop using Genome::Command::Base.

Its features are now in UR's Command::V2.
Remove Genome::Command::Base.
Formatting changes to help docs so can be parsed as verbatim POD.
Pull up setting alternate classes to a new Base.
use SeparatedValueReader to read the file TSV-based file
use SeparatedValueWriter to write TSV-based file

In order to use SeparatedValueWriter we need/want the keys of the data
hash to match the pretty names of the headers.  This converts the
surrounding code to use the pretty headers adn then uses the
SeparatedValueWriter to write the file.
Warn if using old GENOME_NO_REQUIRE_USER_VERIFY variable.
Copy status when copying the profile items.
Modify ExtractReadGroup.pm
add unit test
change the naming of temp bam file