Play it again Sam, but double the tempo

• Now runs 2 to 3 times faster due to new threading support in markdup and fixmate 😍
• All required linux binaries are now bundled to simplify container building
• Reinstated TRAVIS testing
• Improved CPU spreading logic for main alignment pipeline stages
• Variants near contig ends will be less likely to be missed due to improved samclip
• Bundled tools now fully python3 compatible