[Fix] correct CIGAR string in SAM format as well as correct header in…#157
Merged
h-2 merged 2 commits intoseqan:lambda3from Jan 30, 2020
Merged
[Fix] correct CIGAR string in SAM format as well as correct header in…#157h-2 merged 2 commits intoseqan:lambda3from
h-2 merged 2 commits intoseqan:lambda3from
Conversation
h-2
reviewed
Jan 30, 2020
Member
h-2
left a comment
There was a problem hiding this comment.
We should not switch to m.qLength, that this the deprecated member. Using r.qLength is the right thing to do, we just need to make sure it has the right value. Or we need to do std::ranges::size(CORRECTseqs[i]). Whatever CORRECT means in the context.
| seqan::resize(subjSeqLengths, globalHolder.indexFile.seqs.size()); | ||
| SEQAN_OMP_PRAGMA(parallel for simd) | ||
| for (size_t i = 0; i < globalHolder.redSbjSeqs.size(); ++i) | ||
| for (size_t i = 0; i < globalHolder.indexFile.seqs.size(); ++i) |
Member
There was a problem hiding this comment.
wow, good catch, this looks really weird!
fe46385 to
b514544
Compare
h-2
approved these changes
Jan 30, 2020
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
… bam format
Already known problem with macth/record qLength entries.
Wrong number of sequences used for the BAM header