[FIX] Wrong alignment score #3043 #3098
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
The latest updates on your projects. Learn more about Vercel for Git ↗︎
|
seqan-actions
added
lint
2 tasks
rrahn
requested review from
a team and
Irallia
and removed request for
a team
rrahn
force-pushed
the
fix/alignment_affine_trace
branch
from
447126b to
eaf671c
Compare
seqan-actions
added
lint
Codecov ReportBase: 98.22% // Head: 98.22% // Decreases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## master #3098 +/- ##
==========================================
- Coverage 98.22% 98.22% -0.01%
==========================================
Files 275 275
Lines 12181 12192 +11
==========================================
+ Hits 11965 11975 +10
- Misses 216 217 +1
Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here. ☔ View full report at Codecov. |
rrahn
changed the title
eseiler
reviewed
Nov 9, 2022
| @@ -18,8 +18,8 @@ static constexpr seqan3::detail::trace_directions N = seqan3::detail::trace_dire | |||
| static constexpr seqan3::detail::trace_directions D = seqan3::detail::trace_directions::diagonal; | |||
| static constexpr seqan3::detail::trace_directions u = seqan3::detail::trace_directions::up; | |||
| static constexpr seqan3::detail::trace_directions l = seqan3::detail::trace_directions::left; | |||
| static constexpr seqan3::detail::trace_directions U = seqan3::detail::trace_directions::up_open; | |||
| static constexpr seqan3::detail::trace_directions L = seqan3::detail::trace_directions::left_open; | |||
| static constexpr seqan3::detail::trace_directions U = seqan3::detail::trace_directions::carry_up_open; | |||
There was a problem hiding this comment.
Changes as to not need to touch every test
| : (best_trace |= previous_cell.horizontal_trace(), diagonal_score); | ||
| diagonal_score = | ||
| (diagonal_score < horizontal_score) | ||
| ? (best_trace = previous_cell.horizontal_trace() | (best_trace & trace_directions::carry_up_open), |
There was a problem hiding this comment.
(best_trace & trace_directions::carry_left_open) is not needed in the above (L 79) case, because the horizontal trace is always set
Irallia
approved these changes
Nov 10, 2022
include/seqan3/alignment/pairwise/detail/policy_affine_gap_with_trace_recursion.hpp
Show resolved
Hide resolved
Added carry bit to up and left open trace directions in order to capture original open signal even if it is overwritten by the orhtogonal direction. In the particular issue the left extension overrites the up open signal in the last column and fifth row. The traceback now follows the vertical or horizontal direction unitl it encounters the carry bit signal.
eseiler
force-pushed
the
fix/alignment_affine_trace
branch
from
6e23815 to
4fe5489
Compare
seqan-actions
added
lint
eseiler
approved these changes
Nov 14, 2022
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Resolves #3043
Added carry bit to up and left open trace directions in order to capture original open signal even if it is overwritten by the orhtogonal direction. In the particular issue the left extension overwrites the
up Opensignal in the last column and fifth row. The traceback now follows the vertical or horizontal direction unitl it encounters the carry bit signal.