Removed b36 defaults from GMT/Somatic/ReadCounts
remove default reference from Genome::Model::Tools::Nimblegen::DesignFromFiles
remove defaults from Genome::Model::Tools::Capture::SomaticModelGroup
remove defaults from Genome::Model::Tools::Somatic::PindelToBed
remove default reference for Model/Tools/Gatk/GermlineIndel
remove default reference from Model::Tools::Analysis::MutationSpectrumSequenceContextPvalue
remove default reference from Genome::Model::Tools::Varscan::CopyNumber
Fixed default values
Merge branch 'default' into gb_master
remove default reference from Music::Pfam
remove default reference information from Genome::Model::Tools::Capture::SomaticVariationGroup
remove default reference from Genome::Model::Tools::Germline::Filtering
remove default paths from Genome::Model::Tools::Somatic::FilterMouseBases
remove default path from Model::Tools::Sv::Pairoscope
Remove InstrumentData/Command/Align*

Removed command-line versions of alignment modules. They are neither
comprehensive nor complete, and they do not appear to be used.
Remove GMT/Validation/SvCalls
allow default name and bool flag
Merge branch 'master' of ssh://git/srv/git/genome
Remove default tsv from GMT/SnpArray/MergeSegments
Fix example_values in GMT/Somatic/ReadCounts.pm