Close Samples

[duncanca]

I have upgraded from v4.4.2 to 6.2.0. Has the close sample option been removed? I am using the ---call_whole_genome and --snp_dist arguments, no errors are generated but the close samples report section is gone. A binary file snp_diffs.db is generated but I am unsure how to visualize this data.

I found the close sample report very useful to quickly identify related cases and I am hoping this will still be supported.

[jodyphelan]

Hi @duncanca ,

In the json files they are available under the key "linked_samples". However I noticed now that this information is not present in the text output so I'll aim to put that back in for the next release

[duncanca]

I see the data in the json file. Thanks for all your work in developing and continuing to improving this tool.

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On Tue, May 7, 2024, 5:12 PM Jody Phelan, ***@***.***> wrote: Hi @duncanca <https://github.com/duncanca> , In the json files they are available under the key "linked_samples". However I noticed now that this information is not present in the text output so I'll aim to put that back in for the next release — Reply to this email directly, view it on GitHub <#352 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACSUIVH6A72SUTZTEZTZTEDZBE7VRAVCNFSM6AAAAABHF7ZG3KVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TGNBXGEZDO> . You are receiving this because you were mentioned.Message ID: ***@***.***>