[FEATURE] Gustaf: SV classification feature initial commit
[INTERNAL] Gustaf: revised breakend trigger, adjusted app tests to ignore breakend output
[INTERNAL] Gustaf: added svtype options, def start/end pos
[INTERNAL] Gustaf: reduced gff out for breakends
[FIX] Gustaf: multiple output of same bp, breakends for paired-end mode
[FIX][FEATURE] Gustaf: wrong breakend out, mult.bp out, no out of artificial bp, tandem del instead of de novo insertion out
[FEATURE] Gustaf: added support of breakends to breakpoints, excluded them from output
[FEATURE] Gustaf: added deletion support for dupl/transl; prepared extended paired-end tests
[INTERNAL] Gustaf: extensive changes to breakpoint coordinates and output
[FEATURE][FIX] Gustaf: separated be and bp list and support, extensive bp position revision
[TEST] Gustaf: adapted tests to new bp coordinates
[INTERNAL] Gustaf: changed default ID for paired-end data to right mate (if IDs are different)
[INTERNAL] Gustaf: removed all command line output
[FIX] Gustaf: output short sequence IDs in vcf and gff output (no whitespaces)
Merge branch 'develop' of https://github.com/seqan/seqan into feature/gustaf_sv_classification
[FIX] Gustaf_sv_classifcation: first merge attempt
[FIX] Gustaf: vcf output imprecise duplications
[FIX] Gustaf: deletion support of duplication when both positions are equal
[FEATURE] Gustaf: added info for similar breakpoints in vcf output
Merge branch 'develop' of github.com:weese/seqan into develop