Adam Orr

Tag handling with --keep-tags creates invalid SAM output

1

Hi, I was attempting to re-align reads that were aligned with another aligner. I was using the `--keep-tags` option, primarily because I have RG tags and OQ tags that I...

`pipx.util` circular import

2

Importing from `pipx.util` fails due to circular dependency unless `pipx.paths` is imported first. It seems `pipx.util` became dependent on `pipx.paths` in #1281. `pipx.paths` then tries to import `pipx_wrap` from `pipx.util`...

[SEQPROV] RefBase file not found () when using NextGenMap with Teaser

1

It looks like the version of ngm packaged with Teaser suffers from this issue: Cibiv/NextGenMap#10 I was able to resolve the issue by configuring Teaser to use the ngm binary...