Create GMT::Analysis::Maf and refactor methods into it

code-deduplication: jweible
Remove useless comments

code-deduplication: jweible
cleanup
Switch IUB method to tolerate translating 'U' to 'T'

Refactors to use Genome::Infor::IUB failed to account for the fact that the
original method accepted 'U.'  Consultation with Dave Larson lead us to believe
that these should not pollute the original IUB functionality, so a new 'rna_safe'
version of the method was created, and things that used the original were
switched over.
clinseq - fix logic that examines previously_discovered_variations_build of input somatic models
make target_region_set_name optional on RnaSeq models
fix test
Merge branch 'master' of ssh://git/srv/git/genome
updated clin-seq update-analysis to handle previously discovered variants more gracefully
Merge branch 'master' of ssh://git/srv/git/genome
this shouldnt have been checked in yet
Merge branch 'master' of ssh://git/srv/git/genome
fix doc output
remove this until its ready
Updated class browser cache.
Updated `genome` tab completion.
add testobj generator for sample
clinseq - add explicit check for all input samples when evaluating pre-existing clinseq models for suitability
TMPDIR not TEMPDIR
add info on how to free space