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Segmentation fault with very simple code #1279
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This happens on cdc0ed1. I did the following to install: git clone [email protected]:pysam-developers/pysam.git
cd pysam/
python -m venv .venv
source .venv/bin/activate
pip install -e . I guess you need to know my libc and stuff? Is there a handy file I can attach? |
$ pip install -e .
Obtaining file:///home/dan/Build/pysam
Installing build dependencies ... done
Checking if build backend supports build_editable ... done
Getting requirements to build editable ... done
Installing backend dependencies ... done
Preparing editable metadata (pyproject.toml) ... done
Building wheels for collected packages: pysam
Building editable for pysam (pyproject.toml) ... \
done
Created wheel for pysam: filename=pysam-0.22.0-0.editable-cp310-cp310-linux_x86_64.whl size=5106 sha256=522a5eaababdd2e259da9d1fbd7257a614a878444f9ae8ea1e6f14fd6e26cdb1
Stored in directory: /tmp/pip-ephem-wheel-cache-pqsis2yg/wheels/cc/c5/bb/65151f5f844856e0716e962c6e8ead0aac4977a7bd496495c3
Successfully built pysam
Installing collected packages: pysam
Successfully installed pysam-0.22.0 |
The file example_0v26.bed.gz has three columns, which Accessing fields that aren't present in the file is supposed to raise a KeyError. So printing This is an off-by-one error in the presence checking that has been present in this code since 2011. Thanks for the easily reproducible bug report. |
Awesome! My pleasure! Thanks for the fix and for the great library! |
I was looking to fix the incorrect documentation here:
https://pysam.readthedocs.io/en/latest/usage.html#working-with-tabix-indexed-files
(Just a couple of minor issues).
I thought I'd better run the latest version of the code from git, and I found that my 'simple test' turned up a segfault...
The output is:
The text was updated successfully, but these errors were encountered: