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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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Fix support for "--doubletGL" argument. #101

Closed ghuls closed 1 year ago

ghuls commented 1 year ago

Fix support for "--doubletGL" argument as described in the help. Before this patch the code would check for "--doubleGL" instead.

ghuls commented 1 year ago

Not sure if it changes anything in the output itself (using --doubletGL or not).

hxj5 commented 1 year ago

Thank you for the PR, I will merge it.

ghuls commented 1 year ago

@hxj5 which output file is --doubletGL supposed to change? I don't see a difference between the output when using --doubletGL or not using it.

hxj5 commented 1 year ago

Hi, adding the --doubletGL option should change the cellSNP.cells.vcf.gz file (the --genotype option needs to be added in order to output the file). When the option is added, the doublet GT likelihood would be kept in the PL field. This option was initially designed for vireo, we may mark it as deprecated in the future.