Hi,
Thank you for developing this tool, we are working with version 1.5.6
While running straglr with these options
--nprocs 26
--genotype_in_size
--tmpdir "."
--include_partials
--loci bedfile
on ONT data straglr raise:
File "/usr/local/lib/python3.12/site-packages/src/tre.py", line 1216, in get_alleles
Variant.genotype(variant, self.clustering, use_mean=self.use_mean, sex=self.sex, report_in_size=self.genotype_in_size)
File "/usr/local/lib/python3.12/site-packages/src/variant.py", line 82, in genotype
biggest_partial_size = max([r[4] for r in big_partials])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
when '--include_partials' is missing everything goes well,
Best,
JB
Hi,
Thank you for developing this tool, we are working with version 1.5.6
While running straglr with these options
--nprocs 26
--genotype_in_size
--tmpdir "."
--include_partials
--loci bedfile
on ONT data straglr raise:
File "/usr/local/lib/python3.12/site-packages/src/tre.py", line 1216, in get_alleles
Variant.genotype(variant, self.clustering, use_mean=self.use_mean, sex=self.sex, report_in_size=self.genotype_in_size)
File "/usr/local/lib/python3.12/site-packages/src/variant.py", line 82, in genotype
biggest_partial_size = max([r[4] for r in big_partials])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
when '--include_partials' is missing everything goes well,
Best,
JB