Bug fixes and post analysis routines

Improvements & additions

• Modified API to support clonotype table post-analysis routines
• Basic statistical analysis of somatic hypermutations (Analyze module, see readme)
• Clonotype tree construction (Analyze module, see readme)

Fixes

• Fixed exception with P-segment alignment
• Optimized mutation annotation

Known bugs

• --by-read analysis is not working, use 1.0.1 version or later