Support URL inputs in taffy view -r and the Python API#85
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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>
glennhickey
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May 28, 2026
Pulls in #85 (URL inputs), #86 (BlockReader / direct-MAF readers), #87 (faster MAF/TAF emitter+parser via byte-level LW_put* API), and #88 (-T/--threads bgzf_mt across all commands). Conflicts resolved: * Makefile -- union of build deps (kept tui.o + ONElib.o from unitaf, added block_reader.o + remote_io.o from main). * taf_index.c -- short-flag clash: main's -T = --threads collided with unitaf's -T = --tmpDir. Renamed --tmpDir to -d to keep -T/--threads consistent across every command; --tmpDir long form is unchanged so only short-flag callers break. * taf_view.c -- combined #include "tui.h" + "remote_io.h"; gated the .tui auto-detect on !input_is_url (no remote-.tui resolver yet); routed the non-tui else branch through tai_path_for / open_tai_for_reading so URL inputs work there. * taffy/impl/line_iterator.{h,c} -- header auto-merged (LI_get_position from unitaf + LW_put* buffer fields from main). .c kept both the LI_get_position definition and LW_BUF_TARGET. * taffy/impl/maf.c -- both branches hand-rolled the MAF "s" parser. Kept unitaf's body (uses the digit-only maf_parse_u64, ~13% CPU win over strtoll, plus defensive `continue` on malformed lines instead of assertion) and dropped main's now-unused maf_parse_s_line helper. Switched maf_write_block2 to main's LW_put* API (64 KB coalescing via the shared writer) and dropped the file-local maf_lw_putn / maf_i64_str helpers + the bgzf.h include they pulled in. * taffy/impl/taf.c -- auto-merged. Tests: C unit suite 32/32, pytest tai+tui 983/983 pass. Co-Authored-By: Claude Opus 4.7 <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.