Changelog

Features:

• SViper is now a CMake based project
• all functionality of polishing a variant is now outsourced in the include header under the namespace sviper and can also be included as a small header-only library instead of using the app
• SViper can now handle the advanced cigar operations (= and X)
• The thread parameter can be set over the command line
• SViper now outputs a polished VCF with results in the quality and filter fields.
• SViper is now fully parallelized with multiple file handles.

Fixes:

• Negative SV lengths in VCF record are also accepted and parsed correctly
• Some fixes to parsing the cigar string

Introduces SViper as a (almost) stand-alone c++ application instead of a pipeline.

Replaced BAM/FASTA/INDEX manipulation using the SeqAn library.
The external program Pilon is not needed anymore for polishing.