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zhanxw / seqminer

Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R
http://zhanxw.github.io/seqminer/
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not being able to read a tabix file over http #27

Open Asppagh opened 1 year ago

Asppagh commented 1 year ago

Hi, I have problem reading the seqminer::tabix.read.table function to read from http over AWS S3 storage. I get the following error:

[khttp_connect_file] fail to open file (HTTP code: 0). Cannot open specified tabix file:

However, With the same setting, I don't get any error using tabix tool itself. Could anyone give me any clue what could be the cause of this error? Thanks

zhanxw commented 1 year ago

That’s because tabix is build upon the latest htslib which is not incorporated/implemented in seqminer yet. I have several deadlines and cannot implement it right now. Sorry about that. Sent from my iPhoneOn Jan 26, 2023, at 1:53 PM, Ahmad.Samiei @.***> wrote: Hi, I have problem reading the seqminer::tabix.read.table function to read from http over AWS S3 storage. I get the following error: [khttp_connect_file] fail to open file (HTTP code: 0). Cannot open specified tabix file: However, With the same setting, I don't get any error using tabix tool itself. Could anyone give me any clue what could be the cause of this error? Thanks

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