Marcel Martin

Avoid counting the seeds

1

Strobealign currently does two passes over the reference to generate the randstrobes vector: First it counts how many randstrobes there are for each scaffold (parallelized by scaffold) in order to...

Map paired-end reads that overlap each other’s 5' ends

2

As has come up in #317 reported by @y9c, when mapping paired-end reads, we should allow for the case that reads overlap in this way: ``` R1 --------> R2

Try other syncmer hash functions

14

Strobealign currently uses [xxh64](https://github.com/ksahlin/strobealign/blob/8a0e047a451f4ff0ae74988f32695de0a0c80ea4/src/randstrobes.cpp#L38) to hash syncmers. We could switch to a different, faster hash function as long as accuracy is at least as good as now. These are some...

Thanks to a suggestion by @telmin, I spent some time on creating a clang-format configuration and (as a test for now) reformatted the codebase with it. In the Python world,...

Does --interleaved need to support mixed input?

2

Hi @luispedro. I was just looking into #273, which is about the `--interleaved` option. It currently allows mixing single ends with paired ends. One issue with the current implementation is...

Alignment with ksw2/WFA2 - Take 2

6

This supersedes #242 and is a much smaller PR because the refactoring has already been done in #249. As before: - Use WFA2 to align the NAM itself - Use...

The current test dataset consists of the first 100'000 reads of SRR6055476. As it is real sequencing data, we do not have the truth available and thus cannot assess accuracy....

Determine whether re-estimating insert size distribution for each chunk changes accuracy

1

As discussed in #168

Sometimes `ssw_align()` is asked to compute an alignment for a reference sequence longer than 2000 bp here: https://github.com/ksahlin/strobealign/blob/8d3ef7e113abe9159a38343d970e864fc5afaab4/src/aln.cpp#L35-L43 This gets triggered in the Drosophila test dataset for read `@SRR6055476.50009`. The...

### Describe the bug I encountered a compiler crash when attempting to re-declare a loop variable as as cdef variable after the loop. Cython first correctly complains about what is...