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EichlerLab / pav

Phased assembly variant caller
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module ‘analib.pd’ has no attribute 'read_csv_chrom' #3

Closed PengJia6 closed 3 years ago

PengJia6 commented 3 years ago

Hi,

Thanks for developing such an excellent pipeline!

I found the asmlib.call.merge_haplotypes function in rule call_merge_haplotypes was errored because the missing of read_csv_chrom in analib.pd.

I used the lastest verision of analib in svpop.

Best, Peng Jia

paudano commented 3 years ago

The version of PAV is out of sync with SV-Pop in the dep directory. analib.pd.read_csv_chrom() (in SV-Pop) is a newer function that PAV expects. I need to make the dependencies into a submodule to keep them in sync. I'll let you know when that's done, then you can pull a new version of PAV and run it.

PengJia6 commented 3 years ago

Thanks a lot! Best, Peng

paudano commented 3 years ago

I am working out a bug that over-trims contig alignments and leads to severely reduced sensitivity. As soon as that is tested, I'll push the update. Thanks for your patience!

PengJia6 commented 3 years ago

Thanks for your reminder! I look forward to seeing the new update!

BTW, pav provides 2 aligner (lra and minimap2) for contig mapping, which one do you recommend?

paudano commented 3 years ago

Those dependencies (kanapy and SV-Pop) are now submodules:

git clone --recursive https://github.com/EichlerLab/pav.git

That should take care of the problem you were having.

See README.md for other Python and external dependencies.

There are some other fixes in this, which took some time to test. Thank you for your patience!