Marcel Martin
Marcel Martin
The `--info-file` option should be used instead. Also document how to turn an info file into an equivalent rest file.
Possible solution: Add an option `--info-file-paired` to write a second info file.
The discussion in #76 reminded me of an idea I had a while ago for possibly improving performance when dealing with many SequenceRecord objects: We could implement some kind of...
and also `Sequence.comment` and perhaps `Sequence.sep`. They could be lazily computed. Perhaps also add `.header` as an alias for `.name`? Should setting `.id` and `.comment` be supported? Convenient, but perhaps...
It would be great if StrobeAlign could (optionally) add an `@RG` header and `RG` tags to each read. Having RG tags is a requirement in some of our pipelines and...
The program exits with a segfault when the reference FASTA file does not exist: ``` $ strobealign ref.fasta dummy.fasta ... Unique strobemers: 1 Total time generating flat vector: 3.2896e-05 s...
This adds support for linking against WFA2-lib in StrobeAlign. I’ve added the C++ demo program from WFA2-lib as `src/wfademo.cpp` and it works (this should of course be removed again). I...
From a comment in `aln.cpp`: > I created an entire new function here, duplicating a lot of the code as outputting secondary hits is has some overhead to the >...
By default, StrobeAlign outputs no secondary alignments (`-N 0`). I’ve tried to see what happens on the test dataset when using `-N 1` and `-N 2`. The sixth read (`SRR1377138.6`)...