Comments (6)
Dear @jamesdalg,
Thank you very much for pointing this out. We will incorporate this to our next release.
Regards,
Yekai
from duet.
@yekaizhou Let me know when this is addressed. My group is almost specifically asking for SNP aware SV detection and I can't really give them the great phased results duet would bring without it. Sniffles gives a great deal of indels and duet addresses this.
from duet.
The inconsistency of the numpy library is fixed in our latest release v1.0.
from duet.
I'm getting the same error about AttributeError: module 'numpy' has no attribute 'int'.
(And no variant calls from Clair3).
I've tried downloading the latest release (v 1.0) and substituting that for the line git clone https://github.com/yekaizhou/duet.git
in the installation instructions. And then running pip install .
in the folder with the new version.
However, I'm still getting the same error so I'm wondering if I'm doing something wrong with the installation of the latest release?
from duet.
Hi @haraldgrove, could you please also try to replace two "np.int" instances to "int" in /your_conda_env/duet/bin/preprocess/CreateTensorPileupFromCffi.py (line 141 and 142)?
from duet.
That seems to have fixed the issue, thanks for the help.
from duet.
Related Issues (13)
- SNP calling not working HOT 6
- Compatibility with SURVIVOR HOT 5
- Request: A docker image with duet HOT 3
- Combining calls from multiple samples
- Feature request: control for clair3 parameters HOT 4
- Increase support for species with. different number of chromosome HOT 2
- pinned bcftools version libcrypto.so.1.0.0: issue HOT 4
- [Enhancement] Sniffles as extra sv_caller HOT 3
- SNP phasing not running HOT 6
- Feature enhancement: ability to provide sample name for VCF HOT 1
- error when run the duet demo data HOT 6
- Could not load dynamic library 'libcudart.so.11.0'; dlerror: HOT 2
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