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Bioconductor / GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.
http://bioconductor.github.io/GenomicDataCommons/
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legacy error while running slicing #111

Closed SinhaI closed 1 year ago

SinhaI commented 1 year ago

Hi, While running slicing function I am getting an error message.

slicing("df80679e-c4d3-487b-934c-fcc782e5d46e", regions="chr17:75000000-76000000", token = GDC_TOKEN, overwrite = TRUE, legacy = FALSE)

Error in if (legacy) .Deprecated(msg = paste0("The 'legacy' argument is deprecated.\n", : the condition has length > 1

I have a valid token from GDC. Thanks for your help.

LiNk-NY commented 1 year ago

Thank you for reporting. I will take a look.

LiNk-NY commented 1 year ago

Can you try the latest version on GitHub? 1.25.2? Thank you.

SinhaI commented 1 year ago

Hi, after using version 1.25.2 from GitHub now I am getting below error.

Error in .gdc_post(endpoint = sprintf("slicing/view/%s", uuid), add_headers('Content-type' = "application/json"), : Not Found (HTTP 404).

Thanks.

LiNk-NY commented 1 year ago

Hi @SinhaI Did you see here? https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/#http-error-codes It looks like the ID cannot be found. Are you using a legacy file?

SinhaI commented 1 year ago

Hi, Thanks for your reply. Now the code is working fine for me. I was trying to slice several .bam files. After checking the list I realized that few of the files are transcriptome bam files for which slicing is not working. It's working fine for genomic bam files.

Slicing for genomic bam files was not working while using an earlier version of GenomicDataCommons however it worked fine while using GitHub version 1.25.2. Thanks.

LiNk-NY commented 1 year ago

I am not sure if the transcriptome bam files are slice-able. You could ask the GDC Help Desk : support@nci-gdc.datacommons.io