[Alignment Config] Change align_cfg::gap to align_cfg::gap_cost_affine

[rrahn]

Description

We remove the gap cost scheme and implement a direct high-level configuration element for the affine gap scheme.

Here is the proposed change of the interface:

seqan3::align_cfg::gap_cost_affine    [optional]

construction

seqan3::align_cfg::gap_cost_affine affine{seqan3::align_cfg::open_score{-10}, seqan3::align_cfg::extension_score{-1}};

later access and set

affine.open_score = seqan3::align_cfg::open_score{-10};
affine.extension_score = seqan3::align_cfg::extension_score{-1};

or by seqan::get

auto && affine = seqan3::get<seqan3::align_cfg::gap_cost_affine>(config);
affine.open_score = seqan3::align_cfg::open_score{-10};
affine.extension_score = seqan3::align_cfg::extension_score{-1};

query if configuration was piped

config_t::template exists<seqan3::align_cfg::gap_cost_affine>()

Acceptance Criteria

• All of the alignment works with the changed align_cfg::gap_cost_affine

Tasks

• Add an implementation for the align_cfg::gap_cost_affine
• Make the basic tests for the new configuration element
• Replace any occurrence of align_cfg::gap with the new config
• Remove old align_cfg::gap configuration
• Update the documentation and snippets accordingly
• Deprecate gap_scheme

Definition of Done

• Implementation and design approved
• Unit tests pass
• Test coverage = 100%
• Microbenchmarks added and/or affected microbenchmarks < 5% performance drop
• API documentation added
• Tutorial/teaching material added
• Test suite compiles in less than 30 seconds (on travis)
• Changelog entry added