Support URL inputs in taffy view -r and the Python API#85
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glennhickey wants to merge 1 commit intomainfrom
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Support URL inputs in taffy view -r and the Python API#85glennhickey wants to merge 1 commit intomainfrom
glennhickey wants to merge 1 commit intomainfrom
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Routes URL inputs (http://, https://, s3://, ...) through htslib's
URL-aware bgzf_open, so a region query against a remote MAF/TAF only
fetches the .tai plus the BGZF blocks the iterator actually needs.
- LI_construct_from_path: thin wrapper over bgzf_open, used in lieu of
fopen+LI_construct when the input is a URL
- remote_io.{h,c}: URL detector + .tai slurp helper that writes the
fetched bytes to a tmpfile (so downstream LI_construct(FILE*) can
fileno() it)
- taf_view.c: detects URL inputs, requires -r, falls through to the
shared cleanup path
- Python: AlignmentReader and TafIndex accept URL strings; URL-backed
readers skip the per-FILE* close that would otherwise corrupt
- Clear error message when htslib was built without libcurl, with a
pointer to ./configure --enable-libcurl
- README note documenting the htslib-with-libcurl requirement
Verified against a 184 GB MAF on S3: a 500 bp slice returns the right
content in ~8 s, dominated by the 5.9 MB index fetch.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Use htslib to support inputs over http. Seems to work pretty well thugh applied only to indexed taffy view (-r) queries for now.
These work by downloading the entire .tai, loading it into memory, then reading only the selected range from the remote alignment file.
Some things I need to check before merging: cactus integration (inc static build) and if it works on Mac.