I am trying to pull regions from a bunch of BAM files on an online server. I'd like to pull the reads mapping to a certain 1kb or so chunk and download them for analysis. They are far too massive to download them all, and it's impractical even to wget them one at a time and pull the regions out using samtools (tried it, and it worked, but it took forever). Since I'll have to do this for a number of regions that I won't know in advance, I need a better way.
I noticed that samtools is capable of running 'samtools view' off of a web address. Sadly, this data is protected behind an https server, which samtools doesn't know how to handle. I notice that IGV is able to read the BAM files of the net by asking for my login and querying specific regions only that I bring up to view, but I don't have a way of automating the process on hundreds of files.
Does anyone have any ideas of how to run something like samtools view on specific regions over an https connection?