readmanchiu

I've been leery of the among of memory used to create an object for every support read instead of a simple tuple.

```python Traceback (most recent call last): File "/projects/btl_scratch/rchiu/tmp/straglr/extract_repeats.py", line 7, in from dataclasses import dataclass File "/home/rchiu/miniconda2/lib/python3.9/dataclasses.py", line 5, in import inspect File "/home/rchiu/miniconda2/lib/python3.9/inspect.py", line 39, in import importlib.machinery File...

I guess you are interested in running Straglr in targeted mode i.e. passing the locus info to `--loci` In this case, you can specify the motif as "CA*" for the...

Thanks for trying Straglr, @MaestSi It has been my assumption that users would want to be notified about interruptions (like the first user) so I thought Straglr reporting these impure...

did you run minimap2 with soft-clipping (`-Y`) enabled? seems like Straglr was trying to extract the potential repeat sequence from the bam file but failed. You should trying testing out...

if you don't mind posting the SAM records of the 2 alignments, it may help me understand why the supplementary alignment was picked over the primary one.

Hi @stefandiederich I don't think you need to always pad your coordinate to get the desired result. You happened to get your "desired" motif when you add some padding as...

@MaestSi, one read should only be used once as support for one locus despite it has multiple alignments. The same read may be used as support for more than 1...

Thanks for trying Straglr. This is my first time seeing amplicon data, and the main issue is that each read can cover >1 locus. This violates my assumption of each...

I think you are using one of the forks out there, as I noticed from the command line there is a `--trf` parameter which is not available from Straglr. I...