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.
Use last_succeeded_build instead of lastest_build
Add new params to sanitize BAM file available since Picard 1.108
Fixes to compilation issues.  Consistant use of hash_ref instead of dereferencing. Add test case.
Add version check for sanitize option.
Remove R library dependency on optparse.
Add correct version parsing.
Remove is_optional when default_value is defined.
A couple class definition changes and an update to the sanitize picard version comparison to include v1.108
Added back a few more is_optional values for default attributes.
Really die if we don't find a subject.
test handling no repeats by copying the input fasta
Updated class browser cache.
Updated `genome` tab completion.
Merge pull request #210 from jasonwalker80/rna_ercc_qc
Merge pull request #246 from jasonwalker80/picard_revert_sam_updates
Merge pull request #253 from tmooney/better_subjectmapping_errors

Really die if we don't find a subject.
minor refactor of handling of no-repetitive sequences detected to give better log file output
remove comment litter