change config and avocado main for basic run
Merge pull request #34 from hammerlab/basic-run

Add input stage to sample configs
Fixes to assembler to get simple SNP calling working.
Upgrading avocado to use adam-0.7.3-SNAPSHOT series of releases.
Merge pull request #28 from fnothaft/assembler-snp-calls

Fixes to assembler to get simple SNP calling working.