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Hi @dpryan79, I tested MethylDackel on bam files for PBAT libraries, and the wrong strand is reported in the output. Can I modify the argument to make MethylDackel detect the...

Thank you @dpryan79 . I did swap the reads in PE mode, and reverse complement the reads in SE mode before before mapping. But it would be nice if there...

Looking forward to have this feature.

@achimnol Thanks you for you work. I seems that `pythonTypeArgs` is not correctly matched. I highlight type annotation with red italic font, thus your can see the bug directly. ...

@lilydjwg Thank you for your reply. I remove `pythonTypeArgs` from *L213* and python list is rendered correctly now. Is there any other bug I didn't notice?

```bash samtools view -F 4 test.sam | sam2pairwise ``` might solve the issue

This issue can be triggered by "readthrough" reads, where insert size is shorter than one of the reads. scheme: ``` ------->

segmentation fault on binary data too... `-st BIN`

Why filterStr1 is different? Can we cache the parsed results?