Error with pairtools 1.0.1

[mblanche]

I just upgraded pairtools in our pipelines to 1.0.1 using pip in a clean docker image using Ubuntu:22.04 and I'm getting the following errors:

Traceback (most recent call last):
    File "/usr/local/bin/pairtools", line 8, in <module>
      sys.exit(cli())
    File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1130, in __call__
      return self.main(*args, **kwargs)
    File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1055, in main
      rv = self.invoke(ctx)
    File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1657, in invoke
      return _process_result(sub_ctx.command.invoke(sub_ctx))
    File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1404, in invoke
      return ctx.invoke(self.callback, **ctx.params)
    File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 760, in invoke
      return __callback(*args, **kwargs)
    File "/usr/local/lib/python3.10/dist-packages/pairtools/cli/__init__.py", line 183, in wrapper
      return func(*args, **kwargs)
    File "/usr/local/lib/python3.10/dist-packages/pairtools/cli/split.py", line 44, in split
      split_py(pairsam_path, output_pairs, output_sam, **kwargs)
    File "/usr/local/lib/python3.10/dist-packages/pairtools/cli/split.py", line 119, in split_py
      sam2 = cols.pop(sam2col)
  IndexError: pop index out of range

Could someone look into this? Pairtools is part of our data delivery pipelines and we're currently stuck.

Thanks

[Phlya]

https://open2c.slack.com/archives/CTWSBFD9U/p1664914811337159?thread_ts=1664914811.337159&cid=CTWSBFD9U check out this discussion on our Slack

[mblanche]

I don't have access to Open2C... Can you expend in this ticket?

[Phlya]

Sorry, I forgot you'd need an invite... https://bit.ly/open2c-slack I think the main conclusion is that this should be fixed in the latest commit to the master branch here.

[mblanche]

Ah, can someone update the PyPi repo? Not great to have a bug in pip installable version...

[Phlya]

You can install from github pip install https://github.com/open2c/pairtools/archive/refs/heads/master.zip

[mblanche]

Thanks I'll do that but still, I would suggest you either remove your broken 1.0.1 repo from PyPi or you fix it. Many folks will fumble on this error...

[Phlya]

It's impossible to remove anything from PyPI AFAIK. We will fix it of course.

[agalitsyna]

pairtools v1.0.2 release is out: https://github.com/open2c/pairtools/releases/tag/v1.0.2 I hope it resolves this problem for you. Otherwise, feel free to re-open and let us know the dataset and your code.