[FEATURE] Add std::string overload for alignment_from_cigar. #3077
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 ↗︎
|
Codecov ReportBase: 98.25% // Head: 98.25% // No change to project coverage 👍
Additional details and impacted files@@ Coverage Diff @@
## master #3077 +/- ##
=======================================
Coverage 98.25% 98.25%
=======================================
Files 276 276
Lines 12344 12344
=======================================
Hits 12128 12128
Misses 216 216
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. |
eseiler
approved these changes
Oct 21, 2022
|
clang-format should be resolved by a rebase on master, but it's not blocking IMO |
smehringer
force-pushed
the
io_alignment_from_cigar_overload
branch
from
ffc7151
to
78e180e
Compare
seqan-actions
added
lint
remyschwab
approved these changes
Oct 31, 2022
eseiler
force-pushed
the
io_alignment_from_cigar_overload
branch
from
78e180e
to
bcfcbc2
Compare
seqan-actions
added
lint
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Outdated suggestions cannot be applied.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.
You might have read a CIGAR string from elsewhere, used our IO with a std::string as type for
field::cigaror want to get the alignment for a secondary alignment which is stores as a string in the tag dictionary.In all those cases, you want to create an alignment from a CIGAR string not a vector, so I added an overload.
Note that the overload currently is not the most efficient one, because it allocates a
std::vector<seqan3::cigar>for convenient use of the other overload. This can be improved by directly parsing the CIGAR string.Alternatively, we could make the function
detail::parse_cigar(not a good name right now), which creates a CIGAR vector out of a CIGAR string, public.