Score prealigned sequences

Open
#3,282 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
cpp
Domain
data

Research direction

Start by reading the alignment configuration and scoring APIs, focusing on method_in_place and hamming_scoring_scheme. Determine whether pre-aligned sequences can be scored through the existing alignment entry points or require a new API. Done means the requested configuration scores pre-aligned sequences correctly, with coverage for the expected behavior.

Written by the indexing model from the issue text.

Description

question

Is it possible to score sequences that have been pre-aligned? Something like seqan3::align_cfg::method_in_place{} | seqan3::align_cfg::scoring_scheme{seqan3::hamming_scoring_scheme{}}

Dominant language
C++
Stars
463
Forks
90
Avg merge
1h 11m
Merged PRs (30d)
3

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

More from seqan/seqan3

All issues in seqan/seqan3

Similar issues

More C++ issues

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.