adding haploid-chromosomes argument to support non-human/non-mouse genomes
Refactor UCSC GapList fetcher
Add in concept of filter for ucsc table
Add ucsc dbsnp and segdup importers
Add dbsnp annotation to new svannot
Merge branch 'vep' into gb_master
MC16s: rm seq platform and subclassing by seq platform; did not rm subclasses
MC16s: add oriented metrics
MC16s: add source to amplicon retruned from iterator
MC16s: add more status msgs for metrics during classification
switch order of start and end in match_part rows
updated ur submodule to 007e133
ClinSeq further updates to Cufflinks DE modules
ClinSeq - Fix last push with errors
genome model copy has --recurse and --start now

Also cosmetic updates to Genome::Model and its input associations.

Added two new environment variables for logging control which will be
used in a subsequent commit.
Merge branch 'master' of ssh://git/srv/git/genome