Sofia

Changes:
- Removed data
- Added command to get template workflows (including data)

Fixes:
- Created manifest file to include data files

Independence update

Changes:
- removed all dependencies on pysam
- made lhc-python a dependency and removed tight coupling
- added travis continuous integration
- converted sofia to package

Fixes:
- fixed all unit tests
- fixed template factory unit test
- changed entity definition syntax

Changes:
- Cleaned up index code for gff, gtf, vcf and fasta
- Removed unused flexible opener code
- Removed dependency on setuptools

Warnings release

Steps can now collect warnings that are reported once the tool is finished. Ideally this will help identify conversion problems.

Changes
- Added Converter warnings
- Added GetGenomicFeatureByPosition warnings
- Added GetMajorTranscriptCodingSequence warnings
- Added drug_id entitiy
- Added Genomic of Drug Sensitivity parser (with universal newline support)
- Added
- Added number_of_variants entity
- Added maf files to genomics template
- Added prt files to genomic template
- Added tabix index support to maf files
- Added None protection to converters
- Changed variants without samples to use empty dict instead of None
- Consolidated entity definition parsing for requested and provided entities

Bug fixes
- Fixed txt iterator bug
- Fixed resource resolution bug
- Fixed info command

New entity release

Changes
- Added variant_impact entity
- Added transcript_id entity
- Added attribute map caching