Feature request: Support remote cram files
wdecoster opened this issue · comments
Hi,
Would you be interested in supporting genotyping from remote cram files? I noticed it only requires to comment out two lines at
Line 70 in d932381
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
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:
Line 465 in d932381
May I ask where your file is stored? I can add more exceptions to the list.
Apologies again for the delay.
Best,
Helia
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
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
Thanks for taking care of this! I will let you know if I encounter issues :)