samtools/tabix with https support?

Question

[Alex Reynolds]

I'd like to run tabix-indexed searches of bam and other samtools-indexed files hosted on HTTPS sites. Do the current development branches build samtools and incorporate tabix indexing such that lookups can be done this way, or are there still special builds required to enable this?

Answer 1

[Pierre Lindenbaum]

(not tested) compile with

./configure --enable-libcurl

?

Answer 2

[John Marshall]

Yes.

You might look at the documentation in the INSTALL files in htslib and samtools, and also at samtools's README.

[Pierre Lindenbaum]

https://github.com/samtools/samtools/blob/master/README.md

[John Marshall]

README.md is a different file containing different information that is less relevant here. The INSTALL and README files I referred to are in the release tarballs that Alex will have downloaded and also in the Git source repositories.