seqan3
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seqan
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
When we remove the alignment field from the SAM file, we need to have a replacement in place to get from a CIGAR string, read from file, to an alignment....
Todo: - [ ] Check documentation Follow Up: - [ ] Do we need to pass the reference sequences now that the `field::alignment` is gone - [ ] Remove `field::offset`
### Does this problem persist on the current master? - [X] I have verified the issue on the current master ### Is there an existing issue for this? - [X]...
This adds a remark on how to set CC and CXX. Also, added a comment about failing to find SDSL even though the problem lies with apple clang. see https://github.com/seqan/seqan3/issues/3046
### Does this problem persist on the current main? - [X] I have verified the issue on the current main ### Is there an existing issue for this? - [X]...
Is it possible with seqan3 to open a .bam file for writing in append mode, so that any records pushed to it get appended to the end, but the file...
Is it possible for seqan3-based programs to use only one CPU? I tried setting `seqan3::contrib::bgzf_thread_count` to 1, but the BAM-reading program still uses 200% CPU according to GNU time: one...
1) How do I test whether a BAM record has a given tag? 2) What happens if a tag value type in a BAM record does not match the expected...
The SAM/BAM handling tutorial (https://docs.seqan.de/seqan3/main_user/tutorial_sam_file.html) is quite helpful, but is missing examples on handling of SAM file headers: how to create them from scratch, how to access them, how to...