Improved merging

Update on merging:

• Improved insertion based merging taking the length into account
• Enabling distance to be a function of the length of the SVs
• Improved output including CIPOS CIEND and additional GT fields
• Tracking of VCF ID through merges
• Report merged sequence information
• Various improvements in output VCF file

Update on filter conversion:

• Bugfix in length threshold if SV len is different than breakpoint distances.

Improvements in merging

Various improvements and adoptions to the new VCF format specs.
Including minor bug fixes and cleaning up.

Bug fixes and added functionality

Bug fixes in output of merge
Adopted to VCF 4.3
Added parser for Assemblytics bed file
Added method to produce pair wise comparison matrix for heat map plot.

Added functionality and interface improvements

Improvements:

• Added Hapcut2 parser to vcf
• Bug fixes from interface change in the simulation
• Merging: carry over support information for multisample files
• Fixed missing information in vcf header
• Deleted code piece that cut out 'chr' from chromosome names

Interface improvements

Improvements:

• Improved the interface to be more user friendly.
• Added comparison using MUMMer based SV detection to VCF overlap.

Bug fix and

Bug fixes:

1. Reference bases SVs simulation and evaluation

Extension:

1. Output information for consensus calling

First release

v1.0.0

Resolved bug in eval:  Unkown type