Feature request: Support remote cram files

[Wouter De Coster]

Hi,

Would you be interested in supporting genotyping from remote cram files? I noticed it only requires to comment out two lines at

LongTR/src/bam_io.cpp

Line 70 in d932381

 if (!file_exists(path)) 

Maybe a --remote flag that disables checking if the file exists? Happy to try a PR, but I'm not a C++ programmer.

Thanks,
Wouter

[Helia (Helyaneh) Ziaei Jam]

Hi Wouter,

I apologize for my delayed response. We try to do a minimum check for local files to inform users if their input address is wrong, but I added exceptions here for remote files:

LongTR/src/bam_io.h

Line 465 in d932381

 bool file_exists(const std::string& path){ 

May I ask where your file is stored? I can add more exceptions to the list.

Apologies again for the delay.

Best,
Helia

[Wouter De Coster]

Hi Helia,

Thank you!

The files of interest are available over https and s3:
e.g.: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1KG_ONT_VIENNA/hg38/HG00096.hg38.cram or https://s3.amazonaws.com/1000g-ont/ALIGNMENT_AND_ASSEMBLY_DATA/100_PLUS/IN-HOUSE_MINIMAP2/HG00097-ONT-hg38-R10-LSK114-dorado034_sup_5mCG_5hmCG_v33/HG00097-ONT-hg38-R10-LSK114-dorado034_sup_5mCG_5hmCG_v33.phased.bam

Wouter

[Helia (Helyaneh) Ziaei Jam]

Hi again,

This should be fixed now, can you please pull the latest version and see if LongTR works on your cram files on FTP?

Best,
Helia

[Wouter De Coster]

Thanks for taking care of this! I will let you know if I encounter issues :)