Chaining from-to: * [x] Chain START-END direct: don't demand non-matches * [x] Test in lower bounds * [x] Test in exact align * [x] Test in exact align_until_cost_limit * [x] Fix in lower bounds * [x] Fix in exact align * [x] Fix in exact align_until_cost_limit * [x] Chain START-ANCHOR direct: don't demand non-matches * [x] Test in lower bounds * [x] Test in exact align * [x] Test in exact align_until_cost_limit * [x] Fix in lower bounds * [x] Fix in exact align * [x] Fix in exact align_until_cost_limit * [x] Chain ANCHOR-END direct: don't demand non-matches * [x] Test in lower bounds * [x] Test in exact align * [x] Test in exact align_until_cost_limit * [x] Fix in lower bounds * [x] Fix in exact align * [x] Fix in exact align_until_cost_limit * [x] Chain START-END indirect: demand non-matches if both gaps are at least k * [x] Test in lower bounds * [x] Test in exact align * [x] Test in exact align_until_cost_limit * [x] Fix in lower bounds * [x] Fix in exact align * [x] Fix in exact align_until_cost_limit * [x] Chain START-END indirect: don't demand non-matches if one gap is less than k * [x] Test in lower bounds * [x] Test in exact align * [x] Test in exact align_until_cost_limit * [x] Fix in lower bounds * [x] Fix in exact align * [x] Fix in exact align_until_cost_limit * [x] Chain START-ANCHOR indirect: demand non-matches * [x] Test in lower bounds * [x] Test in exact align * [x] Test in exact align_until_cost_limit * [x] Fix in lower bounds * [x] Fix in exact align * [x] Fix in exact align_until_cost_limit * [x] Chain ANCHOR-END indirect: demand non-matches * [x] Test in lower bounds * [x] Test in exact align * [x] Test in exact align_until_cost_limit * [x] Fix in lower bounds * [x] Fix in exact align * [x] Fix in exact align_until_cost_limit * [x] Chain ANCHOR-ANCHOR direct gap-affine primary: forbidden (only k-1 overlap is allowed with zero cost) * [x] Test in lower bounds * [x] Test in exact align * [x] Test in exact align_until_cost_limit * [x] Fix in lower bounds * [x] Fix in exact align * [x] Fix in exact align_until_cost_limit * [x] Chain ANCHOR-ANCHOR indirect gap-affine primary: demand non-matches * [x] Test in lower bounds * [x] Test in exact align * [x] Test in exact align_until_cost_limit * [x] Fix in lower bounds * [x] Fix in exact align * [x] Fix in exact align_until_cost_limit * [x] Chain ANCHOR-ANCHOR direct gap-affine secondary: forbidden (only k-1 overlap is allowed with zero cost) * [x] Test in lower bounds * [x] Test in exact align * [x] Test in exact align_until_cost_limit * [x] Fix in lower bounds * [x] Fix in exact align * [x] Fix in exact align_until_cost_limit * [x] Chain ANCHOR-ANCHOR indirect gap-affine secondary: demand non-matches * [x] Test in lower bounds * [x] Test in exact align * [x] Test in exact align_until_cost_limit * [x] Fix in lower bounds * [x] Fix in exact align * [x] Fix in exact align_until_cost_limit
Chaining from-to: