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CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets
MIT License
491 stars 190 forks source link

`filter-out` option no work for SE reads #453

Closed y9c closed 3 years ago

timedreamer commented 3 years ago

Hi, I'm facing this problem also. Any solutions so far? I got the error UnboundLocalError: local variable 'read1' referenced before assignment

Thanks! Ji

IanSudbery commented 3 years ago

Hi, I just merged the PR from @yech1990 that should fix this. If you are able to install the latest from master, it should work. Let me know if you need help with that.

timedreamer commented 3 years ago

Hey great! If you could help with installing from master, that would be great! I used conda to install before. I can wait for the conda version too, if it doesn't take long. Thanks!

IanSudbery commented 3 years ago

Hi @timedreamer

I don't know how long the conda release will be as @TomSmithCGAT normally rolls these once there are a few changes to bundle up.

To install from master:

  1. Activate your conda environment.
  2. Download/clone the code to any location of your choice with: git clone https://github.com/CGATOxford/UMI-tools.git
  3. Enter the UMI-tools directory: cd UMI-tools
  4. Install: python setup.py install

You can delete the downloaded/cloned directory if you wish at this point.