Ilya Shlyakhter

Unsupported sam headers get silently stripped

2

### 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]...

appending records to a .bam

1

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...

single-thread mode

4

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...

sam tags functions

3

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...

creating SAM file headers

1

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...

alignment slice positions

1

## Platform - SeqAn version: 3.3.0 ## Question Is there a documented way to extract, from a pairwise alignment result, the alignment slice positions (equivalent to the coordinates[] list of...

several same-score pairwise alignments

6

## Platform - SeqAn version: 3.3.0 - Operating system: > Linux bpb23-acc 5.4.0-136-generic #153-Ubuntu SMP Thu Nov 24 15:56:58 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux - Compiler: x86_64-conda-linux-gnu-c++ (conda-forge gcc...

tutorial link broken

1

The link from https://bedtools.readthedocs.io/en/latest/ to http://quinlanlab.org/tutorials/bedtools/bedtools.html under "Tutorial" seems to be broken.

choosing among same-score alignments

5

When there are several different alignments with the best score, how does parasail choose which alignment/traceback to return? Can it enumerate all best-scoring alignments, in the manner of BioPython's Bio.Align.PairwiseAligner?...

flag to print conda-build output to the console

3

Currently conda-build output is only shown in case of failure. This hides e.g. warnings, and makes it harder to track progress. Would it be hard to add a flag to...